CUBIC Columbia University Bioinformatics

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; DOI: 10.1371/journal.pgen.0020029 (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) 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) Domains, motifs, and clusters in the protein universe
J Liu, B Rost
Current Opinion in Chemical Biology, 2003, 7:5-11 (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) Improving fold recognition without folds
D Przybylski, B Rost
Journal of Molecular Biology, 2004, 341:255-269 (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) 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) 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) 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) NLSdb: database of nuclear localization signals
R Nair, P Carter, B Rost
Nucleic Acids Research, 2003, 31:397-399 (abstr, web) Twilight zone of protein sequence alignments
B Rost
Protein Engineering, 1999, 12:85-94 (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) 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)

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, : Sk�vde, 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