Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Alignments grow, secondary structure prediction improves D Przybylski, B Rost Proteins: Structure, Function, and Bioinformatics, 2002, 46:195-205 (abstr, web, pdf) Twilight zone of protein sequence alignments B Rost Protein Engineering, 1999, 12:85-94 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Prediction of protein secondary structure at better than 70% accuracy B Rost, C Sander Journal of Molecular Biology, 1993, 232:584-599 (abstr, web, pdf) CASP6 assessment of contact prediction O Grana, D Baker, RM Maccallum, J Meiler, M Punta, B Rost, ML Tress, A Valencia Proteins, 2005, 61:214-224 (pdf) Critical assessment of methods of protein structure prediction (CASP)-Round 6 J Moult, K Fidelis, B Rost, T Hubbard, A Tramontano Proteins, 2005, 61:3-7 (pdf) CAFASP2: the second critical assessment of fully automated structure prediction methods D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, AR Ortiz, RLJ Dunbrack Proteins: Structure, Function, and Genetics, 2001, 45 Suppl 5:S171-S183 (pdf) Simple jury predicts protein secondary structure best B Rost, P Baldi, G Barton, J Cuff, V Eyrich, D Jones, K Karplus, R King, M Ouali, G Pollastri, D Przybylski CUBIC preprint, 2001, Simple jury predicts protein secondary structure best:5 (abstr, web, pdf) Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics, 1997, Suppl. 1:192-197 (abstr, web, pdf) Novel leverage of structural genomics J Liu, GT Montelione, B Rost Nature Biotechnology, 2007, Novel leverage of structural genomics:in press (abstr, web, som) Distinguishing protein-coding from non-coding RNA through support vector machines J Liu, J Gough, B Rost PLoS Genetics, 2006, 2:e29; 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C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Loopy proteins appear conserved in evolution J Liu, H Tan, B Rost Journal of Molecular Biology, 2002, 322:53-64 (abstr, web, pdf) ISMB/ECCB 2007 T Lengauer, B Morrison McKay, B Rost Bioinformatics, 2007, 23:i1-i4 (pdf) ISMB 2005 HV Jagadish, D States, B Rost Bioinformatics, 2005, 21 Suppl 1:i1-i2 (pdf) AI and Bioinformatics J Glasgow, I Jurisica, B Rost AI Magazine, 2004, 25:7-8 Ismb 2002 J Glasgow, B Rost Bioinformatics, 2002, 18:S1 (pdf) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) CASP6 assessment of contact prediction O Grana, D Baker, RM Maccallum, J Meiler, M Punta, B Rost, ML Tress, A Valencia Proteins, 2005, 61:214-224 (pdf) Critical assessment of methods of protein structure prediction (CASP)-Round 6 J Moult, K Fidelis, B Rost, T Hubbard, A Tramontano Proteins, 2005, 61:3-7 (pdf) CAFASP3 in the spotlight of EVA VA Eyrich, IYY Koh, D Przybylski, O Gra–a, F Pazos, A Valencia, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53 Suppl 6:548-560 (abstr, web, pdf) Long membrane helices and short loops predicted less accurately CP Chen, B Rost Protein Science, 2002, Long membrane helices and short loops predicted less accurately:2766-2773 (abstr, web, pdf) Transmembrane helix predictions revisited CP Chen, A Kernytsky, B Rost Protein Science, 2002, 11:2774-2791 (abstr, web, pdf) Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology, 2002, 318:595-608 (abstr, web, pdf) CAFASP2: the second critical assessment of fully automated structure prediction methods D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, AR Ortiz, RLJ Dunbrack Proteins: Structure, Function, and Genetics, 2001, 45 Suppl 5:S171-S183 (pdf) Simple jury predicts protein secondary structure best B Rost, P Baldi, G Barton, J Cuff, V Eyrich, D Jones, K Karplus, R King, M Ouali, G Pollastri, D Przybylski CUBIC preprint, 2001, Simple jury predicts protein secondary structure best:5 (abstr, web, pdf) Protein fold recognition by prediction-based threading B Rost, R Schneider, C Sander Journal of Molecular Biology, 1997, 270:471-480 (abstr, web, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles G Pollastri, D Przybylski, B Rost, P Baldi Proteins: Structure, Function, and Bioinformatics, 2002, 47:228-235 (pdf) Refining neural network predictions for helical transmembrane proteins by dynamic programming B Rost, R Casadio, P Fariselli in: 'Fourth International Conference on Intelligent Systems for Molecular Biology' (eds. D States, P Agarwal, T Gaasterland, L Hunter, RF Smith), 1996, : St. Louis, M.O., U.S.A.Refining neural network predictions for helical transmembrane proteins by dynamic programming:192-200 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Progress in protein structure prediction? B Rost, C Sander, R Schneider Trends in Biochemical Sciences, 1993, 18:120-123 (abstr, pdf) Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes R Powers, N Mirkovic, S Goldsmith-Fischman, TB Acton, Y Chiang, YJ Huang, L Ma, PK Rajan, JR Cort, MA Kennedy, J Liu, B Rost, B Honig, D Murray, GT Montelione Protein Science, 2005, 14:2849-61 (pdf) The protein target list of the Northeast Structural Genomics Consortium Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione Proteins: Structure, Function, and Bioinformatics, 2004, 56:181-187 (abstr, pdf) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Novel leverage of structural genomics J Liu, GT Montelione, B Rost Nature Biotechnology, 2007, Novel leverage of structural genomics:in press (abstr, web, som) The transcriptional landscape of the mammalian genome P Carninci, et al. Science, 2005, 309:1559-1563 (pdf) Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) The protein target list of the Northeast Structural Genomics Consortium Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione Proteins: Structure, Function, and Bioinformatics, 2004, 56:181-187 (abstr, pdf) Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii JM Aramini, YJ Huang, JR Cort, S Goldsmith-Fischman, R Xiao, LY Shih, CK Ho, J Liu, B Rost, B Honig, MA Kennedy, TB Acton, GT Montelione Protein Science, 2003, 12:2823-2830 (abstr, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Comparing function and structure between entire proteomes J Liu, B Rost Protein Science, 2001, 10:1970-1979 (abstr, web, pdf) Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow, B Rost Nucleic Acids Research, 2006, 34:W186-188 (abstr, web, pdf) PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow, B Rost Nucleic Acids Research, 2006, 34:W186-188 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Role of transmembrane domains in the functions of Fc receptors R Zidovetzki, B Rost, DL Armstrong, I Pecht Journal of Biophysical Chemistry, 2003, 15:555-575 (abstr, pdf) Long membrane helices and short loops predicted less accurately CP Chen, B Rost Protein Science, 2002, Long membrane helices and short loops predicted less accurately:2766-2773 (abstr, web, pdf) State-of-the-art in membrane prediction CP Chen, B Rost Applied Bioinformatics, 2002, 1:21-35 (abstr, web, pdf) State-of-the-art in membrane prediction CP Chen, B Rost Applied Bioinformatics, 2002, 1:21-35 (abstr, web, pdf) Transmembrane helix predictions revisited CP Chen, A Kernytsky, B Rost Protein Science, 2002, 11:2774-2791 (abstr, web, pdf) Transmembrane helix predictions revisited CP Chen, A Kernytsky, B Rost Protein Science, 2002, 11:2774-2791 (abstr, web, pdf) Comparing function and structure between entire proteomes J Liu, B Rost Protein Science, 2001, 10:1970-1979 (abstr, web, pdf) The role of transmembrane domains in the functions of B- and T-cell receptors R Zidovetzki, B Rost, I Pecht Immunology Letters, 1998, 64:97-107 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Refining neural network predictions for helical transmembrane proteins by dynamic programming B Rost, R Casadio, P Fariselli in: 'Fourth International Conference on Intelligent Systems for Molecular Biology' (eds. D States, P Agarwal, T Gaasterland, L Hunter, RF Smith), 1996, : St. Louis, M.O., U.S.A.Refining neural network predictions for helical transmembrane proteins by dynamic programming:192-200 (abstr, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Prediction of helical transmembrane segments at 95% accuracy B Rost, R Casadio, P Fariselli, C Sander Protein Science, 1995, 4:521-533 (abstr, web, pdf) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) EVAcon: a protein contact prediction evaluation service O Grana, VA Eyrich, F Pazos, B Rost, A Valencia Nucleic Acids Res, 2005, 33:W347-51 (pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen, B Rost Nucleic Acids Research, 2003, 31:3293-3295 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Distinguishing protein-coding from non-coding RNA through support vector machines J Liu, J Gough, B Rost PLoS Genetics, 2006, 2:e29; DOI: 10.1371/journal.pgen.0020029 (abstr, web, pdf) Distinguishing protein-coding from non-coding RNA through support vector machines J Liu, J Gough, B Rost PLoS Genetics, 2006, 2:e29; DOI: 10.1371/journal.pgen.0020029 (abstr, web, pdf) The transcriptional landscape of the mammalian genome P Carninci, et al. Science, 2005, 309:1559-1563 (pdf) Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Predicting protein subcellular localization using intelligent systems R Nair, B Rost in: 'In Silico Technology in Drug Target Identification and Validation' (eds. D Leon, S Markel), 2007, Predicting protein subcellular localization using intelligent systems: (abstr, web) PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow, B Rost Nucleic Acids Research, 2006, 34:W186-188 (abstr, web, pdf) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf) CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf) NLProt: extracting protein names and sequences from papers S Mika, B Rost Nucleic Acids Research, 2004, 32:W634-W637 (abstr, web, pdf) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) CAFASP3 in the spotlight of EVA VA Eyrich, IYY Koh, D Przybylski, O Gra–a, F Pazos, A Valencia, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53 Suppl 6:548-560 (abstr, web, pdf) Static benchmarking of membrane helix predictions A Kernytsky, B Rost Nucleic Acids Research, 2003, 31:3642-3644 (abstr, web, pdf) NORSp: predictions of long regions without regular secondary structure J Liu, B Rost Nucleic Acids Research, 2003, 31:3833-3835 (abstr, web, pdf) LOC3D: annotate sub-cellular localization for protein structures R Nair, B Rost Nucleic Acids Research, 2003, 31:3337-3340 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks A Passerini, M Punta, A Ceroni, B Rost, P Frasconi Proteins: Structure, Function, and Bioinformatics, 2006, 65:305-316 (pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Analysing six types of protein-protein interfaces Y Ofran, B Rost Journal of Molecular Biology, 2003, 325:377-387 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) Predicting protein subcellular localization using intelligent systems R Nair, B Rost in: 'In Silico Technology in Drug Target Identification and Validation' (eds. D Leon, S Markel), 2007, Predicting protein subcellular localization using intelligent systems: (abstr, web) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Protein-protein interaction hot spots carved into sequences Y Ofran, B Rost PLoS Computational Biology, 2007, 3:e119 (abstr, web, pdf) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf) Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf) NMPdb: database of nuclear matrix proteins S Mika, B Rost Nucleic Acids Research, 2005, 33:D160-163 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen, B Rost Nucleic Acids Research, 2003, 31:3293-3295 (abstr, web, pdf) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Automatic prediction of protein function B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf) Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811 The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Sequence conserved for sub-cellular localization R Nair, B Rost Protein Science, 2002, 11:2836-2847 (abstr, web, pdf) Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology, 2002, 318:595-608 (abstr, web, pdf) Comparing function and structure between entire proteomes J Liu, B Rost Protein Science, 2001, 10:1970-1979 (abstr, web, pdf) Adaptation of protein surfaces to subcellular location MA Andrade, SI O'Donoghue, B Rost Journal of Molecular Biology, 1998, 276:517-525 (abstr, web, pdf) Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) Novel leverage of structural genomics J Liu, GT Montelione, B Rost Nature Biotechnology, 2007, Novel leverage of structural genomics:in press (abstr, web, som) Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) Outcome of a workshop on archiving structural models of biological macromolecules HM Berman, et al. Structure, 2006, 14:1211-1217 (pdf) Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks A Passerini, M Punta, A Ceroni, B Rost, P Frasconi Proteins: Structure, Function, and Bioinformatics, 2006, 65:305-316 (pdf) Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) CASP6 assessment of contact prediction O Grana, D Baker, RM Maccallum, J Meiler, M Punta, B Rost, ML Tress, A Valencia Proteins, 2005, 61:214-224 (pdf) EVAcon: a protein contact prediction evaluation service O Grana, VA Eyrich, F Pazos, B Rost, A Valencia Nucleic Acids Res, 2005, 33:W347-51 (pdf) Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes R Powers, N Mirkovic, S Goldsmith-Fischman, TB Acton, Y Chiang, YJ Huang, L Ma, PK Rajan, JR Cort, MA Kennedy, J Liu, B Rost, B Honig, D Murray, GT Montelione Protein Science, 2005, 14:2849-61 (pdf) Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes R Powers, N Mirkovic, S Goldsmith-Fischman, TB Acton, Y Chiang, YJ Huang, L Ma, PK Rajan, JR Cort, MA Kennedy, J Liu, B Rost, B Honig, D Murray, GT Montelione Protein Science, 2005, 14:2849-61 (pdf) PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf) 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf) 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) The protein target list of the Northeast Structural Genomics Consortium Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione Proteins: Structure, Function, and Bioinformatics, 2004, 56:181-187 (abstr, pdf) Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web) Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii JM Aramini, YJ Huang, JR Cort, S Goldsmith-Fischman, R Xiao, LY Shih, CK Ho, J Liu, B Rost, B Honig, MA Kennedy, TB Acton, GT Montelione Protein Science, 2003, 12:2823-2830 (abstr, pdf) DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen, B Rost Nucleic Acids Research, 2003, 31:3293-3295 (abstr, web, pdf) Prediction in 1D: secondary structure, membrane helices, and accessibility B Rost Methods Biochem Anal, 2003, 44:559-587 (abstr, web) Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811 The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Reliability of assessment of protein structure prediction methods MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost, A Sali Structure, 2002, 10:435-440 (pdf) Alignments grow, secondary structure prediction improves D Przybylski, B Rost Proteins: Structure, Function, and Bioinformatics, 2002, 46:195-205 (abstr, web, pdf) Protein secondary structure prediction continues to rise B Rost Journal of Structural Biology, 2001, 134:204-218 (abstr, web, pdf) Third generation prediction of secondary structure B Rost, C Sander Methods in Molecular Biology, 2000, 143:71-95 (abstr, web, pdf) Pedestrian guide to analysing sequence databases B Rost, R Schneider CUBIC preprint, 1999, : HeidelbergPedestrian guide to analysing sequence databases:preprint (abstr, web) Adaptation of protein surfaces to subcellular location MA Andrade, SI O'Donoghue, B Rost Journal of Molecular Biology, 1998, 276:517-525 (abstr, web, pdf) Marrying structure and genomics B Rost Structure, 1998, 6:259-263 (abstr, web, pdf) Protein structure prediction in 1D, 2D, and 3D B Rost in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, PR Schreiner), 1998, 3:2242-2255 (abstr, web, pdf) Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics, 1997, Suppl. 1:192-197 (abstr, web, pdf) Learning from evolution to predict protein structure B Rost in: 'BCEC97: Bio-Computing and Emergent Computation' (eds. B Olsson, D Lundh, A Narayanan), 1997, : Skšvde, SwedenLearning from evolution to predict protein structure:87-101 (abstr, web, pdf) NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf) NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf) Protein structures sustain evolutionary drift B Rost Folding & Design, 1997, 2:S19-S24 (abstr, web, pdf) Bridging the protein sequence-structure gap by structure predictions B Rost, C Sander Annual Review of Biophysics and Biomolecular Structure, 1996, 25:113-136 (abstr, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf) Prediction of helical transmembrane segments at 95% accuracy B Rost, R Casadio, P Fariselli, C Sander Protein Science, 1995, 4:521-533 (abstr, web, pdf) Progress of 1D protein structure prediction at last B Rost, C Sander Proteins: Structure, Function, and Genetics, 1995, 23:295-300 (abstr, pdf) Protein structure prediction by neural networks B Rost, C Sander in: 'The handbook of brain theory and neural networks' (eds. M Arbib), 1995, : Cambridge, MAProtein structure prediction by neural networks:772-775 (abstr, pdf) Protein structure prediction by neural networks B Rost, C Sander in: 'The handbook of brain theory and neural networks' (eds. M Arbib), 1995, : Cambridge, MAProtein structure prediction by neural networks:772-775 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) Data based modeling of proteins L Holm, B Rost, C Sander, R Schneider, G Vriend in: 'Statistical Mechanics, Protein Structure, and Protein Substrate Interactions' (eds. S Doniach), 1994, : New YorkData based modeling of proteins:277-296 1D secondary structure prediction through evolutionary profiles B Rost, C Sander in: 'Protein Structure by Distance Analysis' (eds. H Bohr, S Brunak), 1994, : Amsterdam, Oxford, Washington1D secondary structure prediction through evolutionary profiles:257-276 (abstr, pdf) 1D secondary structure prediction through evolutionary profiles B Rost, C Sander in: 'Protein Structure by Distance Analysis' (eds. H Bohr, S Brunak), 1994, : Amsterdam, Oxford, Washington1D secondary structure prediction through evolutionary profiles:257-276 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Evolution and neural networks - protein secondary structure prediction above 71% accuracy B Rost, C Sander, R Schneider in: '27th Hawaii International Conference on System Sciences' (eds. L Hunter), 1994, 5:385-394 (abstr, pdf) Evolution and neural networks - protein secondary structure prediction above 71% accuracy B Rost, C Sander, R Schneider in: '27th Hawaii International Conference on System Sciences' (eds. L Hunter), 1994, 5:385-394 (abstr, pdf) PHD - an automatic server for protein secondary structure prediction B Rost, C Sander, R Schneider CABIOS, 1994, 10:53-60 (abstr, pdf) Redefining the goals of protein secondary structure prediction B Rost, C Sander, R Schneider Journal of Molecular Biology, 1994, 235:13-26 (abstr, pdf) Structure prediction of proteins - where are we now? B Rost, C Sander Current Opinion in Biotechnology, 1994, 5:372-380 (abstr, pdf) Molecular modelling of the Norrie disease protein predicts a cysteine knot growth factor tertiary structure T Meitinger, A Meindl, P Bork, B Rost, C Sander, M Haasemann, J Murken Nature Genetics, 1993, 5:376-380 (pdf) Improved prediction of protein secondary structure by use of sequence profiles and neural networks B Rost, C Sander Proceedings of the National Academy of Sciences, 1993, 90:7558-7562 (abstr, pdf) Improved prediction of protein secondary structure by use of sequence profiles and neural networks B Rost, C Sander Proceedings of the National Academy of Sciences, 1993, 90:7558-7562 (abstr, pdf) Prediction of protein secondary structure at better than 70% accuracy B Rost, C Sander Journal of Molecular Biology, 1993, 232:584-599 (abstr, web, pdf) Prediction of protein secondary structure at better than 70% accuracy B Rost, C Sander Journal of Molecular Biology, 1993, 232:584-599 (abstr, web, pdf) Progress in protein structure prediction? B Rost, C Sander, R Schneider Trends in Biochemical Sciences, 1993, 18:120-123 (abstr, pdf) Secondary structure prediction of all-helical proteins in two states B Rost, C Sander Protein Engineering, 1993, 6:831-836 (abstr, pdf) Exercising multi-layered networks on protein secondary structure B Rost, C Sander in: 'Neural Networks: From Biology to High Energy Physics' (eds. O Benhar, S Brunak, P DelGiudice, M Grandolfo), 1992, 3:209-220 (abstr, pdf) Exercising multi-layered networks on protein secondary structure B Rost, C Sander in: 'Neural Networks: From Biology to High Energy Physics' (eds. O Benhar, S Brunak, P DelGiudice, M Grandolfo), 1992, 3:209-220 (abstr, pdf) Jury returns on structure prediction B Rost, C Sander Nature, 1992, 360:540 (pdf) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Protein-protein interaction hot spots carved into sequences Y Ofran, B Rost PLoS Computational Biology, 2007, 3:e119 (abstr, web, pdf) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Analysing six types of protein-protein interfaces Y Ofran, B Rost Journal of Molecular Biology, 2003, 325:377-387 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) The transcriptional landscape of the mammalian genome P Carninci, et al. Science, 2005, 309:1559-1563 (pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Predicting protein subcellular localization using intelligent systems R Nair, B Rost in: 'In Silico Technology in Drug Target Identification and Validation' (eds. D Leon, S Markel), 2007, Predicting protein subcellular localization using intelligent systems: (abstr, web) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web) Automatic prediction of protein function B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf) Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811 Role of transmembrane domains in the functions of Fc receptors R Zidovetzki, B Rost, DL Armstrong, I Pecht Journal of Biophysical Chemistry, 2003, 15:555-575 (abstr, pdf) Did evolution leap to create the protein universe? B Rost Current Opinion in Structural Biology, 2002, 12:409-416 (abstr, web, pdf) Third generation prediction of secondary structure B Rost, C Sander Methods in Molecular Biology, 2000, 143:71-95 (abstr, web, pdf) Evolution teaches neural networks B Rost in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau, ML Ristig), 1999, : HeidelbergEvolution teaches neural networks:207-223 (abstr, web, pdf) Pedestrian guide to analysing sequence databases B Rost, R Schneider CUBIC preprint, 1999, : HeidelbergPedestrian guide to analysing sequence databases:preprint (abstr, web) Marrying structure and genomics B Rost Structure, 1998, 6:259-263 (abstr, web, pdf) Protein structure prediction in 1D, 2D, and 3D B Rost in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, PR Schreiner), 1998, 3:2242-2255 (abstr, web, pdf) The role of transmembrane domains in the functions of B- and T-cell receptors R Zidovetzki, B Rost, I Pecht Immunology Letters, 1998, 64:97-107 (abstr, web, pdf) NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf) Sisyphus and prediction of protein structure B Rost, SI O'Donoghue Computer Applications in Biological Science, 1997, 13:345-356 (abstr, web, pdf) Bridging the protein sequence-structure gap by structure predictions B Rost, C Sander Annual Review of Biophysics and Biomolecular Structure, 1996, 25:113-136 (abstr, pdf) Pitfalls of protein sequence analysis B Rost, A Valencia Current Opinion in Biotechnology, 1996, 7:457-461 (abstr, web, pdf) Protein structure prediction by neural networks B Rost, C Sander in: 'The handbook of brain theory and neural networks' (eds. M Arbib), 1995, : Cambridge, MAProtein structure prediction by neural networks:772-775 (abstr, pdf) Structure prediction of proteins - where are we now? B Rost, C Sander Current Opinion in Biotechnology, 1994, 5:372-380 (abstr, pdf) Progress in protein structure prediction? B Rost, C Sander, R Schneider Trends in Biochemical Sciences, 1993, 18:120-123 (abstr, pdf) SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Rising accuracy of protein secondary structure prediction B Rost in: 'Protein structure determination, analysis, and modeling for drug discovery' (eds. D Chasman), 2003, : New YorkRising accuracy of protein secondary structure prediction:207-249 (abstr, web) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles G Pollastri, D Przybylski, B Rost, P Baldi Proteins: Structure, Function, and Bioinformatics, 2002, 47:228-235 (pdf) EVA: large-scale analysis of secondary structure prediction B Rost, V Eyrich Proteins: Structure, Function, and Genetics, 2001, 45 Suppl 5:S192-S199 (abstr, web, pdf) Simple jury predicts protein secondary structure best B Rost, P Baldi, G Barton, J Cuff, V Eyrich, D Jones, K Karplus, R King, M Ouali, G Pollastri, D Przybylski CUBIC preprint, 2001, Simple jury predicts protein secondary structure best:5 (abstr, web, pdf) Evolution teaches neural networks B Rost in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau, ML Ristig), 1999, : HeidelbergEvolution teaches neural networks:207-223 (abstr, web, pdf) A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment A Zemla, C Venclovas, K Fidelis, B Rost Proteins: Structure, Function, and Genetics, 1999, 34:220-223 (pdf) Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics, 1997, Suppl. 1:192-197 (abstr, web, pdf) Learning from evolution to predict protein structure B Rost in: 'BCEC97: Bio-Computing and Emergent Computation' (eds. B Olsson, D Lundh, A Narayanan), 1997, : Skšvde, SwedenLearning from evolution to predict protein structure:87-101 (abstr, web, pdf) NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf) Bridging the protein sequence-structure gap by structure predictions B Rost, C Sander Annual Review of Biophysics and Biomolecular Structure, 1996, 25:113-136 (abstr, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf) Progress of 1D protein structure prediction at last B Rost, C Sander Proteins: Structure, Function, and Genetics, 1995, 23:295-300 (abstr, pdf) Protein structure prediction by neural networks B Rost, C Sander in: 'The handbook of brain theory and neural networks' (eds. M Arbib), 1995, : Cambridge, MAProtein structure prediction by neural networks:772-775 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) 1D secondary structure prediction through evolutionary profiles B Rost, C Sander in: 'Protein Structure by Distance Analysis' (eds. H Bohr, S Brunak), 1994, : Amsterdam, Oxford, Washington1D secondary structure prediction through evolutionary profiles:257-276 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Evolution and neural networks - protein secondary structure prediction above 71% accuracy B Rost, C Sander, R Schneider in: '27th Hawaii International Conference on System Sciences' (eds. L Hunter), 1994, 5:385-394 (abstr, pdf) PHD - an automatic server for protein secondary structure prediction B Rost, C Sander, R Schneider CABIOS, 1994, 10:53-60 (abstr, pdf) Redefining the goals of protein secondary structure prediction B Rost, C Sander, R Schneider Journal of Molecular Biology, 1994, 235:13-26 (abstr, pdf) Improved prediction of protein secondary structure by use of sequence profiles and neural networks B Rost, C Sander Proceedings of the National Academy of Sciences, 1993, 90:7558-7562 (abstr, pdf) Prediction of protein secondary structure at better than 70% accuracy B Rost, C Sander Journal of Molecular Biology, 1993, 232:584-599 (abstr, web, pdf) Progress in protein structure prediction? B Rost, C Sander, R Schneider Trends in Biochemical Sciences, 1993, 18:120-123 (abstr, pdf) Secondary structure prediction of all-helical proteins in two states B Rost, C Sander Protein Engineering, 1993, 6:831-836 (abstr, pdf) Exercising multi-layered networks on protein secondary structure B Rost, C Sander in: 'Neural Networks: From Biology to High Energy Physics' (eds. O Benhar, S Brunak, P DelGiudice, M Grandolfo), 1992, 3:209-220 (abstr, pdf) SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) The transcriptional landscape of the mammalian genome P Carninci, et al. Science, 2005, 309:1559-1563 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) A platform for integrating threading results with protein family analyses F Pazos, B Rost, A Valencia Bioinformatics, 1999, 15:1062-1063 (abstr, web, pdf) Short yeast ORFs: expressed protein or not? B Rost CUBIC preprint, 1999, Short yeast ORFs: expressed protein or not?: (web) Marrying structure and genomics B Rost Structure, 1998, 6:259-263 (abstr, web, pdf) Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf) SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics, 1997, Suppl. 1:192-197 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) Conservation and prediction of solvent accessibility in protein families B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 20:216-226 (abstr, pdf) Novel leverage of structural genomics J Liu, GT Montelione, B Rost Nature Biotechnology, 2007, Novel leverage of structural genomics:in press (abstr, web, som) Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf) Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web) Prediction in 1D: secondary structure, membrane helices, and accessibility B Rost Methods Biochem Anal, 2003, 44:559-587 (abstr, web) Target space for structural genomics revisited J Liu, B Rost Bioinformatics, 2002, 18:922-933 (abstr, web, pdf) Marrying structure and genomics B Rost Structure, 1998, 6:259-263 (abstr, web, pdf) Predicting protein subcellular localization using intelligent systems R Nair, B Rost in: 'In Silico Technology in Drug Target Identification and Validation' (eds. D Leon, S Markel), 2007, Predicting protein subcellular localization using intelligent systems: (abstr, web) Predicting protein subcellular localization using intelligent systems R Nair, B Rost in: 'In Silico Technology in Drug Target Identification and Validation' (eds. D Leon, S Markel), 2007, Predicting protein subcellular localization using intelligent systems: (abstr, web) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) NMPdb: database of nuclear matrix proteins S Mika, B Rost Nucleic Acids Research, 2005, 33:D160-163 (abstr, web, pdf) NMPdb: database of nuclear matrix proteins S Mika, B Rost Nucleic Acids Research, 2005, 33:D160-163 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Automatic prediction of protein function B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Sequence conserved for sub-cellular localization R Nair, B Rost Protein Science, 2002, 11:2836-2847 (abstr, web, pdf) Finding nuclear localisation signals M Cokol, R Nair, B Rost EMBO Reports, 2000, 1:411-415 (abstr, web, pdf) Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) Effective use of sequence correlation and conservation in fold recognition O Olmea, B Rost, A Valencia Journal of Molecular Biology, 1999, 293:1221-1239 (abstr, web, pdf) Protein fold recognition by prediction-based threading B Rost, R Schneider, C Sander Journal of Molecular Biology, 1997, 270:471-480 (abstr, web, pdf) Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) CUBIC: Results / Papers (by Category) Page index:   Alignment methods   CASP   Clustering proteins   Comparative modelling   Databases   Disorder   Editorial   Evaluation of prediction methods   Evolution   Experimental structure   Flexibility   Genomics predictions   Membrane regions   Methods   Non-coding RNA   Prediction services   Protein binding   Protein function   Protein structure   Protein-protein interaction   Protemic predictions   Reviews   Secondary structure   Sequence analysis   Solvent accessibility   Structural genomics   Subcellular localization   Threading (remote homology) Publication index - Sorted by year - Sorted by authors - Collected abstracts Publications by Category (topic/keyword) Alignment methods:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) Distinguishing protein-coding from non-coding RNA through support vector machines J Liu, J Gough, B Rost PLoS Genetics, 2006, 2:e29; DOI: 10.1371/journal.pgen.0020029 (abstr, web, pdf) CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) Alignments grow, secondary structure prediction improves D Przybylski, B Rost Proteins: Structure, Function, and Bioinformatics, 2002, 46:195-205 (abstr, web, pdf) Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology, 2002, 318:595-608 (abstr, web, pdf) Twilight zone of protein sequence alignments B Rost Protein Engineering, 1999, 12:85-94 (abstr, web, pdf) Refining neural network predictions for helical transmembrane proteins by dynamic programming B Rost, R Casadio, P Fariselli in: 'Fourth International Conference on Intelligent Systems for Molecular Biology' (eds. D States, P Agarwal, T Gaasterland, L Hunter, RF Smith), 1996, : St. Louis, M.O., U.S.A.Refining neural network predictions for helical transmembrane proteins by dynamic programming:192-200 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) Improved prediction of protein secondary structure by use of sequence profiles and neural networks B Rost, C Sander Proceedings of the National Academy of Sciences, 1993, 90:7558-7562 (abstr, pdf) Progress in protein structure prediction? B Rost, C Sander, R Schneider Trends in Biochemical Sciences, 1993, 18:120-123 (abstr, pdf) CASP:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material CASP6 assessment of contact prediction O Grana, D Baker, RM Maccallum, J Meiler, M Punta, B Rost, ML Tress, A Valencia Proteins, 2005, 61:214-224 (pdf) CAFASP3 in the spotlight of EVA VA Eyrich, IYY Koh, D Przybylski, O Gra–a, F Pazos, A Valencia, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53 Suppl 6:548-560 (abstr, web, pdf) EVA: large-scale analysis of secondary structure prediction B Rost, V Eyrich Proteins: Structure, Function, and Genetics, 2001, 45 Suppl 5:S192-S199 (abstr, web, pdf) CAFASP-1: critical assessment of fully automated structure prediction methods D Fischer, C Barret, K Bryson, A Elofsson, A Godzik, D Jones, KJ Karplus, LA Kelley, RM MacCallum, K Pawowski, B Rost, L Rychlewski, M Sternberg Proteins: Structure, Function, and Genetics, 1999, Suppl 3:209-217 (pdf) Clustering proteins:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) Domains, motifs, and clusters in the protein universe J Liu, B Rost Current Opinion in Chemical Biology, 2003, 7:5-11 (abstr, web, pdf) Comparative modelling:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Outcome of a workshop on archiving structural models of biological macromolecules HM Berman, et al. Structure, 2006, 14:1211-1217 (pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Data based modeling of proteins L Holm, B Rost, C Sander, R Schneider, G Vriend in: 'Statistical Mechanics, Protein Structure, and Protein Substrate Interactions' (eds. S Doniach), 1994, : New YorkData based modeling of proteins:277-296 Databases:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material NMPdb: database of nuclear matrix proteins S Mika, B Rost Nucleic Acids Research, 2005, 33:D160-163 (abstr, web, pdf) PEP: Predictions for Entire Proteomes P Carter, J Liu, B Rost Nucleic Acids Research, 2003, 31:410-413 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Marrying structure and genomics B Rost Structure, 1998, 6:259-263 (abstr, web, pdf) Disorder:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Editorial:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material ISMB/ECCB 2007: The premier conference on computational biology T Lengauer, B Morrison McKay, B Rost PLoS Computational Biology, 2007, 3:e96 (pdf) Critical assessment of methods of protein structure prediction (CASP)-Round 6 J Moult, K Fidelis, B Rost, T Hubbard, A Tramontano Proteins, 2005, 61:3-7 (pdf) The protein target list of the Northeast Structural Genomics Consortium Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione Proteins: Structure, Function, and Bioinformatics, 2004, 56:181-187 (abstr, pdf) Bioinformatics in structural genomics B Rost, B Honig, A Valencia Bioinformatics, 2002, 18:897 (abstr, web, pdf) Evaluation of prediction methods:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) EVAcon: a protein contact prediction evaluation service O Grana, VA Eyrich, F Pazos, B Rost, A Valencia Nucleic Acids Res, 2005, 33:W347-51 (pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) State-of-the-art in membrane prediction CP Chen, B Rost Applied Bioinformatics, 2002, 1:21-35 (abstr, web, pdf) Reliability of assessment of protein structure prediction methods MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost, A Sali Structure, 2002, 10:435-440 (pdf) EVA: continuous automatic evaluation of protein structure prediction servers V Eyrich, MA Mart’-Renom, D Przybylski, A Fiser, F Pazos, A Valencia, A Sali, B Rost Bioinformatics, 2001, 17:1242-1243 (abstr, web, pdf) EVA: large-scale analysis of secondary structure prediction B Rost, V Eyrich Proteins: Structure, Function, and Genetics, 2001, 45 Suppl 5:S192-S199 (abstr, web, pdf) A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment A Zemla, C Venclovas, K Fidelis, B Rost Proteins: Structure, Function, and Genetics, 1999, 34:220-223 (pdf) Progress of 1D protein structure prediction at last B Rost, C Sander Proteins: Structure, Function, and Genetics, 1995, 23:295-300 (abstr, pdf) Redefining the goals of protein secondary structure prediction B Rost, C Sander, R Schneider Journal of Molecular Biology, 1994, 235:13-26 (abstr, pdf) Evolution:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Protein-protein interaction hot spots carved into sequences Y Ofran, B Rost PLoS Computational Biology, 2007, 3:e119 (abstr, web, pdf) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Sequence conserved for sub-cellular localization R Nair, B Rost Protein Science, 2002, 11:2836-2847 (abstr, web, pdf) Protein structures sustain evolutionary drift B Rost Folding & Design, 1997, 2:S19-S24 (abstr, web, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Prediction of protein secondary structure at better than 70% accuracy B Rost, C Sander Journal of Molecular Biology, 1993, 232:584-599 (abstr, web, pdf) Experimental structure:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf) Flexibility:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen, B Rost Nucleic Acids Research, 2003, 31:3293-3295 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Genomics predictions:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material The transcriptional landscape of the mammalian genome P Carninci, et al. Science, 2005, 309:1559-1563 (pdf) Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes R Powers, N Mirkovic, S Goldsmith-Fischman, TB Acton, Y Chiang, YJ Huang, L Ma, PK Rajan, JR Cort, MA Kennedy, J Liu, B Rost, B Honig, D Murray, GT Montelione Protein Science, 2005, 14:2849-61 (pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf) Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web) Prediction in 1D: secondary structure, membrane helices, and accessibility B Rost Methods Biochem Anal, 2003, 44:559-587 (abstr, web) Target space for structural genomics revisited J Liu, B Rost Bioinformatics, 2002, 18:922-933 (abstr, web, pdf) Marrying structure and genomics B Rost Structure, 1998, 6:259-263 (abstr, web, pdf) Membrane regions:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow, B Rost Nucleic Acids Research, 2006, 34:W186-188 (abstr, web, pdf) PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow, B Rost Nucleic Acids Research, 2006, 34:W186-188 (abstr, web, pdf) PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow, B Rost Nucleic Acids Research, 2006, 34:W186-188 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Role of transmembrane domains in the functions of Fc receptors R Zidovetzki, B Rost, DL Armstrong, I Pecht Journal of Biophysical Chemistry, 2003, 15:555-575 (abstr, pdf) Long membrane helices and short loops predicted less accurately CP Chen, B Rost Protein Science, 2002, Long membrane helices and short loops predicted less accurately:2766-2773 (abstr, web, pdf) Long membrane helices and short loops predicted less accurately CP Chen, B Rost Protein Science, 2002, Long membrane helices and short loops predicted less accurately:2766-2773 (abstr, web, pdf) State-of-the-art in membrane prediction CP Chen, B Rost Applied Bioinformatics, 2002, 1:21-35 (abstr, web, pdf) State-of-the-art in membrane prediction CP Chen, B Rost Applied Bioinformatics, 2002, 1:21-35 (abstr, web, pdf) Transmembrane helix predictions revisited CP Chen, A Kernytsky, B Rost Protein Science, 2002, 11:2774-2791 (abstr, web, pdf) Target space for structural genomics revisited J Liu, B Rost Bioinformatics, 2002, 18:922-933 (abstr, web, pdf) The role of transmembrane domains in the functions of B- and T-cell receptors R Zidovetzki, B Rost, I Pecht Immunology Letters, 1998, 64:97-107 (abstr, web, pdf) Learning from evolution to predict protein structure B Rost in: 'BCEC97: Bio-Computing and Emergent Computation' (eds. B Olsson, D Lundh, A Narayanan), 1997, : Skšvde, SwedenLearning from evolution to predict protein structure:87-101 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Refining neural network predictions for helical transmembrane proteins by dynamic programming B Rost, R Casadio, P Fariselli in: 'Fourth International Conference on Intelligent Systems for Molecular Biology' (eds. D States, P Agarwal, T Gaasterland, L Hunter, RF Smith), 1996, : St. Louis, M.O., U.S.A.Refining neural network predictions for helical transmembrane proteins by dynamic programming:192-200 (abstr, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Prediction of helical transmembrane segments at 95% accuracy B Rost, R Casadio, P Fariselli, C Sander Protein Science, 1995, 4:521-533 (abstr, web, pdf) Prediction of helical transmembrane segments at 95% accuracy B Rost, R Casadio, P Fariselli, C Sander Protein Science, 1995, 4:521-533 (abstr, web, pdf) Methods:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) Distinguishing protein-coding from non-coding RNA through support vector machines J Liu, J Gough, B Rost PLoS Genetics, 2006, 2:e29; DOI: 10.1371/journal.pgen.0020029 (abstr, web, pdf) CASP6 assessment of contact prediction O Grana, D Baker, RM Maccallum, J Meiler, M Punta, B Rost, ML Tress, A Valencia Proteins, 2005, 61:214-224 (pdf) Critical assessment of methods of protein structure prediction (CASP)-Round 6 J Moult, K Fidelis, B Rost, T Hubbard, A Tramontano Proteins, 2005, 61:3-7 (pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Non-coding RNA:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Distinguishing protein-coding from non-coding RNA through support vector machines J Liu, J Gough, B Rost PLoS Genetics, 2006, 2:e29; DOI: 10.1371/journal.pgen.0020029 (abstr, web, pdf) The transcriptional landscape of the mammalian genome P Carninci, et al. Science, 2005, 309:1559-1563 (pdf) Prediction services:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow, B Rost Nucleic Acids Research, 2006, 34:W186-188 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) Protein names peeled precisely off free text S Mika, B Rost Bioinformatics, 2004, 20:I241-I247 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) META-PP: single interface to crucial prediction servers VA Eyrich, B Rost Nucleic Acids Research, 2003, 31:3308-3310 (abstr, web, pdf) EVA: evaluation of protein structure prediction servers IYY Koh, VA Eyrich, MA Marti-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Grana, A Valencia, A Sali, B Rost Nucleic Acids Research, 2003, 31:3311-3315 (abstr, web, pdf) UniqueProt: creating representative protein sequence sets S Mika, B Rost Nucleic Acids Research, 2003, 31:3789-3791 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Protein binding:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks A Passerini, M Punta, A Ceroni, B Rost, P Frasconi Proteins: Structure, Function, and Bioinformatics, 2006, 65:305-316 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Finding nuclear localisation signals M Cokol, R Nair, B Rost EMBO Reports, 2000, 1:411-415 (abstr, web, pdf) Protein function:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) Predicting protein subcellular localization using intelligent systems R Nair, B Rost in: 'In Silico Technology in Drug Target Identification and Validation' (eds. D Leon, S Markel), 2007, Predicting protein subcellular localization using intelligent systems: (abstr, web) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Protein-protein interaction hot spots carved into sequences Y Ofran, B Rost PLoS Computational Biology, 2007, 3:e119 (abstr, web, pdf) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks A Passerini, M Punta, A Ceroni, B Rost, P Frasconi Proteins: Structure, Function, and Bioinformatics, 2006, 65:305-316 (pdf) Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) NMPdb: database of nuclear matrix proteins S Mika, B Rost Nucleic Acids Research, 2005, 33:D160-163 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Predict protein-protein interaction sites from local sequence information Y Ofran, B Rost FEBS Letters, 2003, 544:236-239 (abstr, web, pdf) Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811 The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Sequence conserved for sub-cellular localization R Nair, B Rost Protein Science, 2002, 11:2836-2847 (abstr, web, pdf) Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology, 2002, 318:595-608 (abstr, web, pdf) Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology, 2002, 318:595-608 (abstr, web, pdf) Adaptation of protein surfaces to subcellular location MA Andrade, SI O'Donoghue, B Rost Journal of Molecular Biology, 1998, 276:517-525 (abstr, web, pdf) Prediction of helical transmembrane segments at 95% accuracy B Rost, R Casadio, P Fariselli, C Sander Protein Science, 1995, 4:521-533 (abstr, web, pdf) Protein structure:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg, B Rost Nucleic Acids Research, 2007, 35:3823-3835 (abstr, web, pdf) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks A Passerini, M Punta, A Ceroni, B Rost, P Frasconi Proteins: Structure, Function, and Bioinformatics, 2006, 65:305-316 (pdf) Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav, B Rost Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) PROFbval: predict flexible and rigid residues in proteins A Schlessinger, G Yachdav, B Rost Bioinformatics, 2006, 22:891-893 (abstr, web, pdf, som) CASP6 assessment of contact prediction O Grana, D Baker, RM Maccallum, J Meiler, M Punta, B Rost, ML Tress, A Valencia Proteins, 2005, 61:214-224 (pdf) EVAcon: a protein contact prediction evaluation service O Grana, VA Eyrich, F Pazos, B Rost, A Valencia Nucleic Acids Res, 2005, 33:W347-51 (pdf) Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes R Powers, N Mirkovic, S Goldsmith-Fischman, TB Acton, Y Chiang, YJ Huang, L Ma, PK Rajan, JR Cort, MA Kennedy, J Liu, B Rost, B Honig, D Murray, GT Montelione Protein Science, 2005, 14:2849-61 (pdf) PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf) PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf) 1H, 13C and 15N assignments for the Archaeglobus fulgidis protein AF2095 R Powers, TB Acton, Y Chiang, PK Rajan, JR Cort, MA Kennedy, J Liu, L Ma, B Rost, GT Montelione Journal of Biomolecular NMR, 2004, 30:107-108 (pdf) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web) Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web) Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii JM Aramini, YJ Huang, JR Cort, S Goldsmith-Fischman, R Xiao, LY Shih, CK Ho, J Liu, B Rost, B Honig, MA Kennedy, TB Acton, GT Montelione Protein Science, 2003, 12:2823-2830 (abstr, pdf) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811 Rising accuracy of protein secondary structure prediction B Rost in: 'Protein structure determination, analysis, and modeling for drug discovery' (eds. D Chasman), 2003, : New YorkRising accuracy of protein secondary structure prediction:207-249 (abstr, web) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Target space for structural genomics revisited J Liu, B Rost Bioinformatics, 2002, 18:922-933 (abstr, web, pdf) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles G Pollastri, D Przybylski, B Rost, P Baldi Proteins: Structure, Function, and Bioinformatics, 2002, 47:228-235 (pdf) EVA: large-scale analysis of secondary structure prediction B Rost, V Eyrich Proteins: Structure, Function, and Genetics, 2001, 45 Suppl 5:S192-S199 (abstr, web, pdf) Simple jury predicts protein secondary structure best B Rost, P Baldi, G Barton, J Cuff, V Eyrich, D Jones, K Karplus, R King, M Ouali, G Pollastri, D Przybylski CUBIC preprint, 2001, Simple jury predicts protein secondary structure best:5 (abstr, web, pdf) Evolution teaches neural networks B Rost in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau, ML Ristig), 1999, : HeidelbergEvolution teaches neural networks:207-223 (abstr, web, pdf) A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment A Zemla, C Venclovas, K Fidelis, B Rost Proteins: Structure, Function, and Genetics, 1999, 34:220-223 (pdf) Adaptation of protein surfaces to subcellular location MA Andrade, SI O'Donoghue, B Rost Journal of Molecular Biology, 1998, 276:517-525 (abstr, web, pdf) Marrying structure and genomics B Rost Structure, 1998, 6:259-263 (abstr, web, pdf) Protein structure prediction in 1D, 2D, and 3D B Rost in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, PR Schreiner), 1998, 3:2242-2255 (abstr, web, pdf) Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics, 1997, Suppl. 1:192-197 (abstr, web, pdf) Learning from evolution to predict protein structure B Rost in: 'BCEC97: Bio-Computing and Emergent Computation' (eds. B Olsson, D Lundh, A Narayanan), 1997, : Skšvde, SwedenLearning from evolution to predict protein structure:87-101 (abstr, web, pdf) NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf) Protein fold recognition by prediction-based threading B Rost, R Schneider, C Sander Journal of Molecular Biology, 1997, 270:471-480 (abstr, web, pdf) Sisyphus and prediction of protein structure B Rost, SI O'Donoghue Computer Applications in Biological Science, 1997, 13:345-356 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Refining neural network predictions for helical transmembrane proteins by dynamic programming B Rost, R Casadio, P Fariselli in: 'Fourth International Conference on Intelligent Systems for Molecular Biology' (eds. D States, P Agarwal, T Gaasterland, L Hunter, RF Smith), 1996, : St. Louis, M.O., U.S.A.Refining neural network predictions for helical transmembrane proteins by dynamic programming:192-200 (abstr, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf) Prediction of helical transmembrane segments at 95% accuracy B Rost, R Casadio, P Fariselli, C Sander Protein Science, 1995, 4:521-533 (abstr, web, pdf) Progress of 1D protein structure prediction at last B Rost, C Sander Proteins: Structure, Function, and Genetics, 1995, 23:295-300 (abstr, pdf) Progress of 1D protein structure prediction at last B Rost, C Sander Proteins: Structure, Function, and Genetics, 1995, 23:295-300 (abstr, pdf) Protein structure prediction by neural networks B Rost, C Sander in: 'The handbook of brain theory and neural networks' (eds. M Arbib), 1995, : Cambridge, MAProtein structure prediction by neural networks:772-775 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) Data based modeling of proteins L Holm, B Rost, C Sander, R Schneider, G Vriend in: 'Statistical Mechanics, Protein Structure, and Protein Substrate Interactions' (eds. S Doniach), 1994, : New YorkData based modeling of proteins:277-296 1D secondary structure prediction through evolutionary profiles B Rost, C Sander in: 'Protein Structure by Distance Analysis' (eds. H Bohr, S Brunak), 1994, : Amsterdam, Oxford, Washington1D secondary structure prediction through evolutionary profiles:257-276 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Conservation and prediction of solvent accessibility in protein families B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 20:216-226 (abstr, pdf) Evolution and neural networks - protein secondary structure prediction above 71% accuracy B Rost, C Sander, R Schneider in: '27th Hawaii International Conference on System Sciences' (eds. L Hunter), 1994, 5:385-394 (abstr, pdf) PHD - an automatic server for protein secondary structure prediction B Rost, C Sander, R Schneider CABIOS, 1994, 10:53-60 (abstr, pdf) PHD - an automatic server for protein secondary structure prediction B Rost, C Sander, R Schneider CABIOS, 1994, 10:53-60 (abstr, pdf) Redefining the goals of protein secondary structure prediction B Rost, C Sander, R Schneider Journal of Molecular Biology, 1994, 235:13-26 (abstr, pdf) Structure prediction of proteins - where are we now? B Rost, C Sander Current Opinion in Biotechnology, 1994, 5:372-380 (abstr, pdf) Molecular modelling of the Norrie disease protein predicts a cysteine knot growth factor tertiary structure T Meitinger, A Meindl, P Bork, B Rost, C Sander, M Haasemann, J Murken Nature Genetics, 1993, 5:376-380 (pdf) Improved prediction of protein secondary structure by use of sequence profiles and neural networks B Rost, C Sander Proceedings of the National Academy of Sciences, 1993, 90:7558-7562 (abstr, pdf) Neural networks in chemistry B Rost, G Vriend Chemical Design Autamation News, 1993, 8:24-27 (pdf) Prediction of protein secondary structure at better than 70% accuracy B Rost, C Sander Journal of Molecular Biology, 1993, 232:584-599 (abstr, web, pdf) Progress in protein structure prediction? B Rost, C Sander, R Schneider Trends in Biochemical Sciences, 1993, 18:120-123 (abstr, pdf) Secondary structure prediction of all-helical proteins in two states B Rost, C Sander Protein Engineering, 1993, 6:831-836 (abstr, pdf) Secondary structure prediction of all-helical proteins in two states B Rost, C Sander Protein Engineering, 1993, 6:831-836 (abstr, pdf) Exercising multi-layered networks on protein secondary structure B Rost, C Sander in: 'Neural Networks: From Biology to High Energy Physics' (eds. O Benhar, S Brunak, P DelGiudice, M Grandolfo), 1992, 3:209-220 (abstr, pdf) Jury returns on structure prediction B Rost, C Sander Nature, 1992, 360:540 (pdf) Protein-protein interaction:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (abstr, web, pdf) Protein-protein interaction hot spots carved into sequences Y Ofran, B Rost PLoS Computational Biology, 2007, 3:e119 (abstr, web, pdf) Protein-protein interaction hot spots carved into sequences Y Ofran, B Rost PLoS Computational Biology, 2007, 3:e119 (abstr, web, pdf) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Protein-protein interactions more conserved within species than across species S Mika, B Rost PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Analysing six types of protein-protein interfaces Y Ofran, B Rost Journal of Molecular Biology, 2003, 325:377-387 (abstr, web, pdf) Predict protein-protein interaction sites from local sequence information Y Ofran, B Rost FEBS Letters, 2003, 544:236-239 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Protemic predictions:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Distinguishing protein-coding from non-coding RNA through support vector machines J Liu, J Gough, B Rost PLoS Genetics, 2006, 2:e29; DOI: 10.1371/journal.pgen.0020029 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Prediction of transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski, B Rost Nucleic Acids Research, 2004, 32:2566-2577 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) Short yeast ORFs: expressed protein or not? B Rost CUBIC preprint, 1999, Short yeast ORFs: expressed protein or not?: (web) Reviews:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Online tools for predicting integral membrane proteins H Bigelow, B Rost in: 'Proteomic analysis of membrane proteins: methods and protocols' (eds. MJ Peirce, R Wait), 2007, : Totowa, NJOnline tools for predicting integral membrane proteins: (abstr, web) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Predictive methods using protein sequence Y Ofran, B Rost in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) Domains, motifs, and clusters in the protein universe J Liu, B Rost Current Opinion in Chemical Biology, 2003, 7:5-11 (abstr, web, pdf) Prediction in 1D: secondary structure, membrane helices, and accessibility B Rost Methods Biochem Anal, 2003, 44:559-587 (abstr, web) Rising accuracy of protein secondary structure prediction B Rost in: 'Protein structure determination, analysis, and modeling for drug discovery' (eds. D Chasman), 2003, : New YorkRising accuracy of protein secondary structure prediction:207-249 (abstr, web) State-of-the-art in membrane prediction CP Chen, B Rost Applied Bioinformatics, 2002, 1:21-35 (abstr, web, pdf) Protein secondary structure prediction continues to rise B Rost Journal of Structural Biology, 2001, 134:204-218 (abstr, web, pdf) Evolution teaches neural networks B Rost in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau, ML Ristig), 1999, : HeidelbergEvolution teaches neural networks:207-223 (abstr, web, pdf) Pedestrian guide to analysing sequence databases B Rost, R Schneider CUBIC preprint, 1999, : HeidelbergPedestrian guide to analysing sequence databases:preprint (abstr, web) Pedestrian guide to analysing sequence databases B Rost, R Schneider CUBIC preprint, 1999, : HeidelbergPedestrian guide to analysing sequence databases:preprint (abstr, web) Protein structure prediction in 1D, 2D, and 3D B Rost in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, PR Schreiner), 1998, 3:2242-2255 (abstr, web, pdf) Protein structure prediction in 1D, 2D, and 3D B Rost in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, PR Schreiner), 1998, 3:2242-2255 (abstr, web, pdf) Learning from evolution to predict protein structure B Rost in: 'BCEC97: Bio-Computing and Emergent Computation' (eds. B Olsson, D Lundh, A Narayanan), 1997, : Skšvde, SwedenLearning from evolution to predict protein structure:87-101 (abstr, web, pdf) NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf) Sisyphus and prediction of protein structure B Rost, SI O'Donoghue Computer Applications in Biological Science, 1997, 13:345-356 (abstr, web, pdf) Bridging the protein sequence-structure gap by structure predictions B Rost, C Sander Annual Review of Biophysics and Biomolecular Structure, 1996, 25:113-136 (abstr, pdf) Pitfalls of protein sequence analysis B Rost, A Valencia Current Opinion in Biotechnology, 1996, 7:457-461 (abstr, web, pdf) Protein structure prediction by neural networks B Rost, C Sander in: 'The handbook of brain theory and neural networks' (eds. M Arbib), 1995, : Cambridge, MAProtein structure prediction by neural networks:772-775 (abstr, pdf) Neural networks in chemistry B Rost, G Vriend Chemical Design Autamation News, 1993, 8:24-27 (pdf) Progress in protein structure prediction? B Rost, C Sander, R Schneider Trends in Biochemical Sciences, 1993, 18:120-123 (abstr, pdf) Secondary structure:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web) Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility B Rost in: 'Structural Bioinformatics - 2nd Edition' (eds. PE Bourne, H Weissig), 2007, Prediction of protein structure in 1D - Secondary structure, membrane regions, and solvent accessibility: (abstr, web) Natively unstructured regions in proteins identified from contact predictions A Schlessinger, M Punta, B Rost Bioinformatics, 2007, Natively unstructured regions in proteins identified from contact predictions:in press (abstr, web, pdf, som) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 Automatic secondary structure assignment CAF Andersen, B Rost Methods Biochem Anal., 2003, 44:341-363 (abstr, web) Prediction in 1D: secondary structure, membrane helices, and accessibility B Rost Methods Biochem Anal, 2003, 44:559-587 (abstr, web) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak, B Rost Structure, 2002, 10:175-184 (abstr, web, pdf) Alignments grow, secondary structure prediction improves D Przybylski, B Rost Proteins: Structure, Function, and Bioinformatics, 2002, 46:195-205 (abstr, web, pdf) Protein secondary structure prediction continues to rise B Rost Journal of Structural Biology, 2001, 134:204-218 (abstr, web, pdf) Third generation prediction of secondary structure B Rost, C Sander Methods in Molecular Biology, 2000, 143:71-95 (abstr, web, pdf) Pedestrian guide to analysing sequence databases B Rost, R Schneider CUBIC preprint, 1999, : HeidelbergPedestrian guide to analysing sequence databases:preprint (abstr, web) Protein structure prediction in 1D, 2D, and 3D B Rost in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, PR Schreiner), 1998, 3:2242-2255 (abstr, web, pdf) Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics, 1997, Suppl. 1:192-197 (abstr, web, pdf) NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf) Sisyphus and prediction of protein structure B Rost, SI O'Donoghue Computer Applications in Biological Science, 1997, 13:345-356 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio, P Fariselli Protein Science, 1996, 5:1704-1718 (abstr, web, pdf) Progress of 1D protein structure prediction at last B Rost, C Sander Proteins: Structure, Function, and Genetics, 1995, 23:295-300 (abstr, pdf) Protein structure prediction by neural networks B Rost, C Sander in: 'The handbook of brain theory and neural networks' (eds. M Arbib), 1995, : Cambridge, MAProtein structure prediction by neural networks:772-775 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf) 1D secondary structure prediction through evolutionary profiles B Rost, C Sander in: 'Protein Structure by Distance Analysis' (eds. H Bohr, S Brunak), 1994, : Amsterdam, Oxford, Washington1D secondary structure prediction through evolutionary profiles:257-276 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Combining evolutionary information and neural networks to predict protein secondary structure B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 19:55-72 (abstr, pdf) Evolution and neural networks - protein secondary structure prediction above 71% accuracy B Rost, C Sander, R Schneider in: '27th Hawaii International Conference on System Sciences' (eds. L Hunter), 1994, 5:385-394 (abstr, pdf) PHD - an automatic server for protein secondary structure prediction B Rost, C Sander, R Schneider CABIOS, 1994, 10:53-60 (abstr, pdf) Structure prediction of proteins - where are we now? B Rost, C Sander Current Opinion in Biotechnology, 1994, 5:372-380 (abstr, pdf) Improved prediction of protein secondary structure by use of sequence profiles and neural networks B Rost, C Sander Proceedings of the National Academy of Sciences, 1993, 90:7558-7562 (abstr, pdf) Prediction of protein secondary structure at better than 70% accuracy B Rost, C Sander Journal of Molecular Biology, 1993, 232:584-599 (abstr, web, pdf) Secondary structure prediction of all-helical proteins in two states B Rost, C Sander Protein Engineering, 1993, 6:831-836 (abstr, pdf) Exercising multi-layered networks on protein secondary structure B Rost, C Sander in: 'Neural Networks: From Biology to High Energy Physics' (eds. O Benhar, S Brunak, P DelGiudice, M Grandolfo), 1992, 3:209-220 (abstr, pdf) Jury returns on structure prediction B Rost, C Sander Nature, 1992, 360:540 (pdf) Sequence analysis:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material ISIS: Interaction Sites Identified from Sequence Y Ofran, B Rost Bioinformatics, 2007, 23:e13-16 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) The transcriptional landscape of the mammalian genome P Carninci, et al. Science, 2005, 309:1559-1563 (pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook' (eds. JE Walker), 2005, : Totowa NJHow to use protein 1D structure predicted by PROFphd:875-901 CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) Target space for structural genomics revisited J Liu, B Rost Bioinformatics, 2002, 18:922-933 (abstr, web, pdf) Pedestrian guide to analysing sequence databases B Rost, R Schneider CUBIC preprint, 1999, : HeidelbergPedestrian guide to analysing sequence databases:preprint (abstr, web) Twilight zone of protein sequence alignments B Rost Protein Engineering, 1999, 12:85-94 (abstr, web, pdf) Pitfalls of protein sequence analysis B Rost, A Valencia Current Opinion in Biotechnology, 1996, 7:457-461 (abstr, web, pdf) Solvent accessibility:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) Adaptation of protein surfaces to subcellular location MA Andrade, SI O'Donoghue, B Rost Journal of Molecular Biology, 1998, 276:517-525 (abstr, web, pdf) Learning from evolution to predict protein structure B Rost in: 'BCEC97: Bio-Computing and Emergent Computation' (eds. B Olsson, D Lundh, A Narayanan), 1997, : Skšvde, SwedenLearning from evolution to predict protein structure:87-101 (abstr, web, pdf) PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology, 1996, 266:525-539 (abstr, web, pdf) Progress of 1D protein structure prediction at last B Rost, C Sander Proteins: Structure, Function, and Genetics, 1995, 23:295-300 (abstr, pdf) Conservation and prediction of solvent accessibility in protein families B Rost, C Sander Proteins: Structure, Function, and Genetics, 1994, 20:216-226 (abstr, pdf) Structural genomics:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes R Powers, N Mirkovic, S Goldsmith-Fischman, TB Acton, Y Chiang, YJ Huang, L Ma, PK Rajan, JR Cort, MA Kennedy, J Liu, B Rost, B Honig, D Murray, GT Montelione Protein Science, 2005, 14:2849-61 (pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf) CHOP proteins into structural domains J Liu, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 55:678-688 (abstr, web, pdf) Sequence-based prediction of protein domains J Liu, B Rost Nucleic Acids Research, 2004, 32:3522-3530 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) The protein target list of the Northeast Structural Genomics Consortium Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione Proteins: Structure, Function, and Bioinformatics, 2004, 56:181-187 (abstr, pdf) Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii JM Aramini, YJ Huang, JR Cort, S Goldsmith-Fischman, R Xiao, LY Shih, CK Ho, J Liu, B Rost, B Honig, MA Kennedy, TB Acton, GT Montelione Protein Science, 2003, 12:2823-2830 (abstr, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Comparing function and structure between entire proteomes J Liu, B Rost Protein Science, 2001, 10:1970-1979 (abstr, web, pdf) Subcellular localization:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Predicting protein subcellular localization using intelligent systems R Nair, B Rost in: 'In Silico Technology in Drug Target Identification and Validation' (eds. D Leon, S Markel), 2007, Predicting protein subcellular localization using intelligent systems: (abstr, web) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) Create and assess protein networks through molecular characteristics of individual proteins Y Ofran, G Yachdav, E Mozes, T-t Soong, R Nair, B Rost Bioinformatics, 2006, 22:e402-7 (abstr, web, pdf) NMPdb: database of nuclear matrix proteins S Mika, B Rost Nucleic Acids Research, 2005, 33:D160-163 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) Mimicking cellular sorting improves prediction of subcellular localization R Nair, B Rost Journal of Molecular Biology, 2005, 348:85-100 (abstr, web, pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) Annotating protein function through lexical analysis R Nair, B Rost AI Magazine, 2004, 25:45-56 (abstr, web) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair, B Rost Nucleic Acids Research, 2004, 32:W517-W521 (abstr, web, pdf) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Better prediction of sub-cellular localization by combining evolutionary and structural information R Nair, B Rost Proteins: Structure, Function, and Bioinformatics, 2003, 53:917-930 (abstr, web, pdf) Automatic prediction of protein function B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf) The PredictProtein server B Rost, J Liu Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Inferring sub-cellular localisation through automated lexical analysis R Nair, B Rost Bioinformatics, 2002, 18:S78-S86 (abstr, web, pdf) Finding nuclear localisation signals M Cokol, R Nair, B Rost EMBO Reports, 2000, 1:411-415 (abstr, web, pdf) Adaptation of protein surfaces to subcellular location MA Andrade, SI O'Donoghue, B Rost Journal of Molecular Biology, 1998, 276:517-525 (abstr, web, pdf) Threading (remote homology):  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski, B Rost Nucleic Acids Research, 2007, 35:2238-2246 (abstr, web, pdf, som) Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf) A platform for integrating threading results with protein family analyses F Pazos, B Rost, A Valencia Bioinformatics, 1999, 15:1062-1063 (abstr, web, pdf) Update on protein structure prediction: results of the 1995 IRBM workshop T Hubbard, et al. Folding & Design, 1996, 1:R55-R63 (abstr, pdf) Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf)