| Link | Title | Quote |
|---|
| Protein structure
|
| index - www-abstr | Predicting transmembrane beta-barrels for entire proteomes | H Bigelow, D Petrey, J Liu, D Przybylski and B Rost (2004) NAR, volxx, |
| - | Sequence-based prediction of protein domains | J Liu and B Rost (2004) NAR, volxx, submitted |
| - | Improving fold recognition without folds | D Przybylski and B Rost (2004) JMB, volxx, submitted |
| - | Toward good 2D predictions in proteins | M Punta and B Rost (2004) FEBS, volxx, submitted |
| - | CHOP: parsing proteins into structural domains | J Liu and B Rost (2004) Nucl Acids Res, volxx, submitted |
| index - www-abstr | The PredictProtein server | B Rost, G Yachdav and J Liu (2004) Nucl Acids Res, volxx, in_press_pages |
| index - www-abstr-pdf | Transmembrane domains in the functions of Fc receptors | R Zidovetzki, B Rost, DL Armstrong and I Pecht (2003) J Biophys Chem, 15, 555-575 |
| index - www-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 and GT Montelione (2003) Prot Sci, 12, 2823-2830 |
| index - www-abstr-pdf | NORSp: predictions of long regions without regular secondary structure | J Liu and B Rost (2003) Nucl Acids Res, 31, 3833-3835 |
| index - www-abstr-pdf | LOC3D: annotate sub-cellular localization for protein structures | R Nair and B Rost (2003) Nucl Acids Res, 31, 3337-3340 |
| index - www-abstr-pdf | DSSPcont: continuous secondary structure assignments for proteins | P Carter, CAF Andersen and B Rost (2003) Nucl Acids Res, 31, 3293-3295 |
| index - www-abstr-pdf | EVA: evaluation of protein structure prediction servers | IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost (2003) Nucl Acids Res, 31, 3311-3315 |
| index - www-abstr-pdf | CAFASP3 in the spotlight of EVA | VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost (2003) Proteins, 53 S6, 548-560 |
| index - www-abstr-pdf | Better prediction of sub-cellular localization through evolution and structure | R Nair and B Rost (2003) Proteins, 53, 917-930 |
| index - www-abstr-pdf | The PredictProtein server | B Rost and J Liu (2003) Nucl Acids Res, 31, 3300-3304 |
| index - www-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 and P Baldi (2002) Proteins, 47, 228-235 |
| index - www-pdf | Reliability of assessment of protein structure prediction methods | MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost and A Sali (2002) Structure, 10, 435-440 |
| index - www-abstr-pdf | Alignments grow, secondary structure prediction improves | D Przybylski and B Rost (2002) Proteins, 46, 197-205 |
| index - www-abstr-pdf | Continuum secondary structure captures protein flexibility | CAF Andersen, AG Palmer, S Brunak and B Rost (2002) Structure, 10, 175-185 |
| index - www-abstr-pdf | Loopy proteins appear conserved in evolution | J Liu, H Tan and B Rost (2002) J Mol Biol, 322, 53-64 |
| index - www-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 and RLJ Dunbrack (2001) Proteins, 45 Suppl 5, S171-183 |
| index - www-abstr-pdf | EVA: continuous automatic evaluation of protein structure prediction servers | VA Eyrich, MA Marti-Renom, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali, and B. Rost (2001) Bioinformatics, 17, 1242-1243 |
| index - www-abstr-pdf | Surface profiles predict sub-cellular localisation | R Nair and B Rost (2001) New York: Columbia University, Preprint CUBIC_2001_05, May 2001 |
| index - www-abstr-pdf | Simple jury predicts protein secondary structure best | B Rost, P Baldi, G Barton, J Cuff, VA Eyrich, D Jones, K Karplus, R King, G Pollastri and D Przybylski (2001) New York: Columbia University, Preprint CUBIC_2001_10, Oct 2001 |
| index - www-pdf | A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment | A Zemla, C Venclovas, K Fidelis and B Rost (1999) Proteins, 34, 220-223 |
| index - www-abstr-pdf | Adaptation of protein surfaces to subcellular location | MA Andrade, SI O'Donoghue and B Rost (1998) Journal of Molecular Biology, 276, 517-525 |
| index - www-abstr | Midnight zone of protein structure evolution | B Rost, S O'Donoghue and C Sander (1998) |
| index - www-abstr-pdf | Protein fold recognition by prediction-based threading | B Rost, R Schneider and C Sander (1997) Journal of Molecular Biology, 270, 471-480 |
| index - www-abstr-pdf | Protein structures sustain evolutionary drift | B Rost (1997) Folding & Design, 2, S19-S24 |
| index - www-abstr-pdf | Better 1D predictions by experts with machines | B Rost (1997) Proteins, Suppl. 1, 192-197 |
| index - www-abstr-pdf | PHD: predicting one-dimensional protein structure by profile based neural networks | B Rost (1996) Methods in Enzymology, 266, 525-539 |
| index - www-abstr-pdf | Refining neural network predictions for helical transmembrane proteins by dynamic programming | B Rost, R Casadio and P Fariselli (1996) Fourth International Conference on Intelligent Systems for Molecular Biology, 192-200 |
| index - www-abstr-pdf | Topology prediction for helical transmembrane proteins at 86% accuracy | B Rost, R Casadio and P Fariselli (1996) Protein Science, 5, 1704-1718 |
| index-abstr-pdf | Progress of 1D protein structure prediction at last | B Rost and C Sander (1995) Proteins, 23, 295-300 |
| index - www-abstr-pdf | Prediction of helical transmembrane segments at 95% accuracy | B Rost, R Casadio, P Fariselli and C Sander (1995) Protein Science, 4, 521-533 |
| index - www-abstr-pdf | Fitting 1-D predictions into 3-D structures | B Rost (1995) in: 'Protein folds: a distance based approach' (eds. H Bohr and S Brunak), 132-151 |
| index-abstr-pdf | TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures | B Rost (1995) Third International Conference on Intelligent Systems for Molecular Biology, 314-321 |
| index - www-abstr-pdf | PHD - an automatic server for protein secondary structure prediction | B Rost, C Sander and R Schneider (1994) CABIOS, 10, 53-60 |
| index-abstr-pdf | Redefining the goals of protein secondary structure prediction | B Rost, C Sander and R Schneider (1994) Journal of Molecular Biology, 235, 13-26 |
| index-abstr-pdf | 1D secondary structure prediction through evolutionary profiles | B Rost and C Sander (1994) in: 'Protein Structure by Distance Analysis' (eds. H Bohr and S Brunak), 257-276 |
| index - www-abstr-pdf | Combining evolutionary information and neural networks to predict protein secondary structure | B Rost and C Sander (1994) Proteins, 19, 55-72 |
| index - www-abstr-pdf | Conservation and prediction of solvent accessibility in protein families | B Rost and C Sander (1994) Proteins, 20, 216-226 |
| index-abstr-pdf | Improved prediction of protein secondary structure by use of sequence profiles and neural networks | B Rost and C Sander (1993) Proceedings of the National Academy of Sciences, 90, 7558-7562 |
| index - www-abstr-pdf | Prediction of protein secondary structure at better than 70% accuracy | B Rost and C Sander (1993) Journal of Molecular Biology, 232, 584-599 |
| index-abstr-pdf | Secondary structure prediction of all-helical proteins in two states | B Rost and C Sander (1993) Protein Engineering, 6, 831-836 |
| index - www-pdf | Jury returns on structure prediction | B Rost and C Sander (1992) Nature, 360, 540 |
| index-abstr-pdf | Exercising multi-layered networks on protein secondary structure | B Rost and C Sander (1992) Neural Networks: From Biology to High Energy Physics, 3, 209-220 |
| Protein function
|
| index - www-abstr | Annotating proteins from Endoplasmic Reticulum and Golgi apparatus in eukaryotic proteomes | KO Wrzeszczynski and B Rost (2004) Cellular and Molecular Life Sciences, volxx, |
| index - www-abstr | LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets | R Nair and B Rost (2004) Nucl Acids Res, volxx, |
| - | CHOP: parsing proteins into structural domains | J Liu and B Rost (2004) Nucl Acids Res, volxx, submitted |
| index - www-abstr | The PredictProtein server | B Rost, G Yachdav and J Liu (2004) Nucl Acids Res, volxx, in_press_pages |
| index - www-abstr-pdf | Transmembrane domains in the functions of Fc receptors | R Zidovetzki, B Rost, DL Armstrong and I Pecht (2003) J Biophys Chem, 15, 555-575 |
| index - www-abstr-pdf | Analysing six types of protein-protein interfaces | Y Ofran and B Rost (2003) J Mol Biol, 325, 377-387 |
| index - www-abstr-pdf | Local sequence information can predict protein-protein interaction sites | Y Ofran and B Rost (2003) FEBS Let, 544, 236-239 |
| index - www-abstr-pdf | NORSp: predictions of long regions without regular secondary structure | J Liu and B Rost (2003) Nucl Acids Res, 31, 3833-3835 |
| index - www-abstr-pdf | Continuum secondary structure captures protein flexibility | CAF Andersen, AG Palmer, S Brunak and B Rost (2002) Structure, 10, 175-185 |
| index - www-abstr-pdf | Inferring sub-cellular localization through automated lexical analysis | R Nair and B Rost (2002) Bioinformatics, 18:Suppl 1, S78-S86 |
| index - www-abstr-pdf | Loopy proteins appear conserved in evolution | J Liu, H Tan and B Rost (2002) J Mol Biol, 322, 53-64 |
| index - www-abstr-pdf | Enzyme function less conserved than anticipated | B Rost (2002) J Mol Biol, 318, 595-608 |
| index - www-abstr-pdf | Comparing function and structure between entire proteomes | J Liu and B Rost (2001) Protein Science, 10, 1970-1979 |
| index - www-abstr-pdf | Finding nuclear localization signals | M Cokol, R Nair and B Rost (2000) EMBO Reports, 1, 411-415 |
| index - www-abstr-pdf | Adaptation of protein surfaces to subcellular location | MA Andrade, SI O'Donoghue and B Rost (1998) Journal of Molecular Biology, 276, 517-525 |
| index - www-abstr-pdf | Prediction of helical transmembrane segments at 95% accuracy | B Rost, R Casadio, P Fariselli and C Sander (1995) Protein Science, 4, 521-533 |
| index - www-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 and J Murken (1993) Nature Genetics, 5, 376-380 |
| Sub-cellular localization
|
| index - www-abstr | Annotating proteins from Endoplasmic Reticulum and Golgi apparatus in eukaryotic proteomes | KO Wrzeszczynski and B Rost (2004) Cellular and Molecular Life Sciences, volxx, |
| index - www-abstr | LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets | R Nair and B Rost (2004) Nucl Acids Res, volxx, |
| index - www-abstr | NLSdb: database of nuclear localization signals | R Nair, P Carter and B Rost (2003) Nucl Acid Res, 322, 397-399 |
| index - www-abstr-pdf | LOC3D: annotate sub-cellular localization for protein structures | R Nair and B Rost (2003) Nucl Acids Res, 31, 3337-3340 |
| index - www-abstr-pdf | Better prediction of sub-cellular localization through evolution and structure | R Nair and B Rost (2003) Proteins, 53, 917-930 |
| index - www-abstr-pdf | Inferring sub-cellular localization through automated lexical analysis | R Nair and B Rost (2002) Bioinformatics, 18:Suppl 1, S78-S86 |
| index - www-abstr-pdf | Sequence conserved for sub-cellular localization | R Nair and B Rost (2002) Protein Science, 11, 2836-2847 |
| index - www-abstr-pdf | Surface profiles predict sub-cellular localisation | R Nair and B Rost (2001) New York: Columbia University, Preprint CUBIC_2001_05, May 2001 |
| Protein-protein interaction
|
| index - www-abstr-pdf | Analysing six types of protein-protein interfaces | Y Ofran and B Rost (2003) J Mol Biol, 325, 377-387 |
| index - www-abstr-pdf | Local sequence information can predict protein-protein interaction sites | Y Ofran and B Rost (2003) FEBS Let, 544, 236-239 |
| Secondary structure
|
| index - www-abstr-pdf | NORSp: predictions of long regions without regular secondary structure | J Liu and B Rost (2003) Nucl Acids Res, 31, 3833-3835 |
| index - www-abstr-pdf | DSSPcont: continuous secondary structure assignments for proteins | P Carter, CAF Andersen and B Rost (2003) Nucl Acids Res, 31, 3293-3295 |
| index - www-abstr-pdf | The PredictProtein server | B Rost and J Liu (2003) Nucl Acids Res, 31, 3300-3304 |
| index - www-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 and P Baldi (2002) Proteins, 47, 228-235 |
| index - www-abstr-pdf | Alignments grow, secondary structure prediction improves | D Przybylski and B Rost (2002) Proteins, 46, 197-205 |
| index - www-abstr-pdf | Continuum secondary structure captures protein flexibility | CAF Andersen, AG Palmer, S Brunak and B Rost (2002) Structure, 10, 175-185 |
| index - www-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 and RLJ Dunbrack (2001) Proteins, 45 Suppl 5, S171-183 |
| index - www-abstr-pdf | Simple jury predicts protein secondary structure best | B Rost, P Baldi, G Barton, J Cuff, VA Eyrich, D Jones, K Karplus, R King, G Pollastri and D Przybylski (2001) New York: Columbia University, Preprint CUBIC_2001_10, Oct 2001 |
| index - www-pdf | A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment | A Zemla, C Venclovas, K Fidelis and B Rost (1999) Proteins, 34, 220-223 |
| index - www-abstr-pdf | Better 1D predictions by experts with machines | B Rost (1997) Proteins, Suppl. 1, 192-197 |
| index - www-abstr-pdf | PHD: predicting one-dimensional protein structure by profile based neural networks | B Rost (1996) Methods in Enzymology, 266, 525-539 |
| index - www-abstr-pdf | Topology prediction for helical transmembrane proteins at 86% accuracy | B Rost, R Casadio and P Fariselli (1996) Protein Science, 5, 1704-1718 |
| index-abstr-pdf | Progress of 1D protein structure prediction at last | B Rost and C Sander (1995) Proteins, 23, 295-300 |
| index - www-abstr-pdf | PHD - an automatic server for protein secondary structure prediction | B Rost, C Sander and R Schneider (1994) CABIOS, 10, 53-60 |
| index-abstr-pdf | Redefining the goals of protein secondary structure prediction | B Rost, C Sander and R Schneider (1994) Journal of Molecular Biology, 235, 13-26 |
| index-abstr-pdf | 1D secondary structure prediction through evolutionary profiles | B Rost and C Sander (1994) in: 'Protein Structure by Distance Analysis' (eds. H Bohr and S Brunak), 257-276 |
| index - www-abstr-pdf | Combining evolutionary information and neural networks to predict protein secondary structure | B Rost and C Sander (1994) Proteins, 19, 55-72 |
| index-abstr-pdf | Improved prediction of protein secondary structure by use of sequence profiles and neural networks | B Rost and C Sander (1993) Proceedings of the National Academy of Sciences, 90, 7558-7562 |
| index - www-abstr-pdf | Prediction of protein secondary structure at better than 70% accuracy | B Rost and C Sander (1993) Journal of Molecular Biology, 232, 584-599 |
| index-abstr-pdf | Secondary structure prediction of all-helical proteins in two states | B Rost and C Sander (1993) Protein Engineering, 6, 831-836 |
| index - www-pdf | Jury returns on structure prediction | B Rost and C Sander (1992) Nature, 360, 540 |
| index-abstr-pdf | Exercising multi-layered networks on protein secondary structure | B Rost and C Sander (1992) Neural Networks: From Biology to High Energy Physics, 3, 209-220 |
| Solvent accessibility
|
| index - www-abstr-pdf | The PredictProtein server | B Rost and J Liu (2003) Nucl Acids Res, 31, 3300-3304 |
| index - www-abstr-pdf | Alignments grow, secondary structure prediction improves | D Przybylski and B Rost (2002) Proteins, 46, 197-205 |
| index - www-abstr-pdf | Adaptation of protein surfaces to subcellular location | MA Andrade, SI O'Donoghue and B Rost (1998) Journal of Molecular Biology, 276, 517-525 |
| index - www-abstr-pdf | Better 1D predictions by experts with machines | B Rost (1997) Proteins, Suppl. 1, 192-197 |
| index - www-abstr-pdf | PHD: predicting one-dimensional protein structure by profile based neural networks | B Rost (1996) Methods in Enzymology, 266, 525-539 |
| index-abstr-pdf | Progress of 1D protein structure prediction at last | B Rost and C Sander (1995) Proteins, 23, 295-300 |
| index - www-abstr-pdf | Conservation and prediction of solvent accessibility in protein families | B Rost and C Sander (1994) Proteins, 20, 216-226 |
| Transmembrane segments
|
| index - www-abstr-pdf | Transmembrane domains in the functions of Fc receptors | R Zidovetzki, B Rost, DL Armstrong and I Pecht (2003) J Biophys Chem, 15, 555-575 |
| index - www-abstr-pdf | Static benchmarking of membrane helix predictions | A Kernytsky and B Rost (2003) Nucl Acids Res, 31, 3642-3644 |
| index - www-abstr-pdf | The PredictProtein server | B Rost and J Liu (2003) Nucl Acids Res, 31, 3300-3304 |
| index - www-abstr-pdf | Comparing function and structure between entire proteomes | J Liu and B Rost (2001) Protein Science, 10, 1970-1979 |
| index - www-abstr-pdf | The role of transmembrane domains in the functions of B- and T-cell receptors | R Zidovetzki, B Rost and I Pecht (1998) Immunology Letters, 64, 97-107 |
| index - www-abstr-pdf | PHD: predicting one-dimensional protein structure by profile based neural networks | B Rost (1996) Methods in Enzymology, 266, 525-539 |
| index - www-abstr-pdf | Refining neural network predictions for helical transmembrane proteins by dynamic programming | B Rost, R Casadio and P Fariselli (1996) Fourth International Conference on Intelligent Systems for Molecular Biology, 192-200 |
| index - www-abstr-pdf | Topology prediction for helical transmembrane proteins at 86% accuracy | B Rost, R Casadio and P Fariselli (1996) Protein Science, 5, 1704-1718 |
| index - www-abstr-pdf | Prediction of helical transmembrane segments at 95% accuracy | B Rost, R Casadio, P Fariselli and C Sander (1995) Protein Science, 4, 521-533 |
| Threading (remote homology)
|
| - | Improving fold recognition without folds | D Przybylski and B Rost (2004) JMB, volxx, submitted |
| index - www-abstr-pdf | EVA: evaluation of protein structure prediction servers | IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost (2003) Nucl Acids Res, 31, 3311-3315 |
| index - www-abstr-pdf | CAFASP3 in the spotlight of EVA | VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost (2003) Proteins, 53 S6, 548-560 |
| index - www-abstr-pdf | EVA: continuous automatic evaluation of protein structure prediction servers | VA Eyrich, MA Marti-Renom, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali, and B. Rost (2001) Bioinformatics, 17, 1242-1243 |
| index - www-abstr-pdf | A platform for integrating threading results with protein family analyses | F Pazos, B Rost and A Valencia (1999) Bioinformatics, 15, 1062-1063 |
| index - www-abstr-pdf | Effective use of sequence correlation and conservation in fold recognition | O Olmea, B Rost and A Valencia (1999) Journal of Molecular Biology, 293, 1221-1239 |
| index - www-abstr-pdf | Protein fold recognition by prediction-based threading | B Rost, R Schneider and C Sander (1997) Journal of Molecular Biology, 270, 471-480 |
| index - www-abstr-pdf | Update on protein structure prediction: results of the 1995 IRBM workshop | T Hubbard, A Tramontano, G Barton, D Jones, M Sippl, A Valencia, A Lesk, J Moult, B Rost, C Sander, R Schneider, A Lahm, R Leplae, C Buta , M Eisenstein, O Fjellström, H Floeckner, JG Grossmann, J Hansen, M Helmer-Citterich, FS Joergensen, A Marchler-Bauer, J Osuna, J Park, A Reinhardt, L Ribas de Pouplana, A Rojo-Dominguez, V Saudek, J Sinclair, S Sturrock, C Venclovas and C Vinals (1996) Folding & Design, 1, R55-R63 |
| index - www-abstr | Protein fold recognition by merging 1D structure prediction and sequence alignments | B Rost (1996) |
| index - www-abstr-pdf | Fitting 1-D predictions into 3-D structures | B Rost (1995) in: 'Protein folds: a distance based approach' (eds. H Bohr and S Brunak), 132-151 |
| index-abstr-pdf | TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures | B Rost (1995) Third International Conference on Intelligent Systems for Molecular Biology, 314-321 |
| Evolution
|
| index - www-abstr-pdf | Alignments grow, secondary structure prediction improves | D Przybylski and B Rost (2002) Proteins, 46, 197-205 |
| index - www-abstr-pdf | Sequence conserved for sub-cellular localization | R Nair and B Rost (2002) Protein Science, 11, 2836-2847 |
| index - www-abstr-pdf | Enzyme function less conserved than anticipated | B Rost (2002) J Mol Biol, 318, 595-608 |
| index - www-abstr | Midnight zone of protein structure evolution | B Rost, S O'Donoghue and C Sander (1998) |
| index - www-abstr-pdf | Protein structures sustain evolutionary drift | B Rost (1997) Folding & Design, 2, S19-S24 |
| index - www-abstr-pdf | Combining evolutionary information and neural networks to predict protein secondary structure | B Rost and C Sander (1994) Proteins, 19, 55-72 |
| index - www-abstr-pdf | Prediction of protein secondary structure at better than 70% accuracy | B Rost and C Sander (1993) Journal of Molecular Biology, 232, 584-599 |
| Evaluation of prediction methods
|
| index - www-abstr-pdf | Static benchmarking of membrane helix predictions | A Kernytsky and B Rost (2003) Nucl Acids Res, 31, 3642-3644 |
| index - www-abstr-pdf | EVA: evaluation of protein structure prediction servers | IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost (2003) Nucl Acids Res, 31, 3311-3315 |
| index - www-abstr-pdf | CAFASP3 in the spotlight of EVA | VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost (2003) Proteins, 53 S6, 548-560 |
| index - www-pdf | Reliability of assessment of protein structure prediction methods | MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost and A Sali (2002) Structure, 10, 435-440 |
| index - www-abstr-pdf | Transmembrane helix predictions revisited | CP Chen, A Kernytsky and B Rost (2002) Protein Science, 11, 2774-2791 |
| index - www-abstr-pdf | Long membrane helices and short loops predicted less accurately | CP Chen and B Rost (2002) Protein Science, 11, 2766-2773 |
| index - www-abstr-pdf | Enzyme function less conserved than anticipated | B Rost (2002) J Mol Biol, 318, 595-608 |
| index - www-pdf | A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment | A Zemla, C Venclovas, K Fidelis and B Rost (1999) Proteins, 34, 220-223 |
| index - www-abstr-pdf | Protein fold recognition by prediction-based threading | B Rost, R Schneider and C Sander (1997) Journal of Molecular Biology, 270, 471-480 |
| index-abstr-pdf | Progress of 1D protein structure prediction at last | B Rost and C Sander (1995) Proteins, 23, 295-300 |
| index-abstr-pdf | TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures | B Rost (1995) Third International Conference on Intelligent Systems for Molecular Biology, 314-321 |
| index-abstr-pdf | Redefining the goals of protein secondary structure prediction | B Rost, C Sander and R Schneider (1994) Journal of Molecular Biology, 235, 13-26 |
| Clustering proteins
|
| index - www-abstr | 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 and GT Montelione (2004) Proteins, volxx, |
| index - www-abstr | Automatic target selection for structural genomics on eukaryotes | J Liu, H Hegyi, TB Acton, GT Montelione and B Rost (2004) Proteins, volxx, in_press |
| index - www-abstr | CHOP proteins into structural domains | J Liu and B Rost (2004) Proteins, volxx, in_press |
| index - www-abstr-pdf | Target space for structural genomics revisited | J Liu and B Rost (2002) Bioinformatics, 18, 922-933 |
| Alignment methods
|
| - | Improving fold recognition without folds | D Przybylski and B Rost (2004) JMB, volxx, submitted |
| index - www-abstr-pdf | Alignments grow, secondary structure prediction improves | D Przybylski and B Rost (2002) Proteins, 46, 197-205 |
| index - www-abstr-pdf | Twilight zone of protein sequence alignments | B Rost (1999) Protein Engineering, 12, 85-94 |
| index-abstr-pdf | TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures | B Rost (1995) Third International Conference on Intelligent Systems for Molecular Biology, 314-321 |
| Structural genomics
|
| index - www-abstr | 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 and GT Montelione (2004) Proteins, volxx, |
| index - www-abstr | Automatic target selection for structural genomics on eukaryotes | J Liu, H Hegyi, TB Acton, GT Montelione and B Rost (2004) Proteins, volxx, in_press |
| index - www-abstr | CHOP proteins into structural domains | J Liu and B Rost (2004) Proteins, volxx, in_press |
| index - www-abstr | LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets | R Nair and B Rost (2004) Nucl Acids Res, volxx, |
| - | Sequence-based prediction of protein domains | J Liu and B Rost (2004) NAR, volxx, submitted |
| - | CHOP: parsing proteins into structural domains | J Liu and B Rost (2004) Nucl Acids Res, volxx, submitted |
| index - www-abstr | The PredictProtein server | B Rost, G Yachdav and J Liu (2004) Nucl Acids Res, volxx, in_press_pages |
| index - www-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 and GT Montelione (2003) Prot Sci, 12, 2823-2830 |
| index - www-abstr-pdf | PEP: Predictions for Entire Proteomes | P Carter, J Liu and B Rost (2003) Nucl Acid Res, 31, 410-413 |
| www | Bioinformatics in structural genomics | B Rost, B Honig and A Valencia (2002) Bioinformatics, 18, 897 |
| index - www-abstr-pdf | Target space for structural genomics revisited | J Liu and B Rost (2002) Bioinformatics, 18, 922-933 |
| index - www-abstr-pdf | Loopy proteins appear conserved in evolution | J Liu, H Tan and B Rost (2002) J Mol Biol, 322, 53-64 |
| index - www-abstr-pdf | Enzyme function less conserved than anticipated | B Rost (2002) J Mol Biol, 318, 595-608 |
| Protemics predictions
|
| index - www-abstr | 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 and GT Montelione (2004) Proteins, volxx, |
| index - www-abstr | NLSdb: database of nuclear localization signals | R Nair, P Carter and B Rost (2003) Nucl Acid Res, 322, 397-399 |
| index - www-abstr-pdf | PEP: Predictions for Entire Proteomes | P Carter, J Liu and B Rost (2003) Nucl Acid Res, 31, 410-413 |
| index - www-abstr-pdf | Target space for structural genomics revisited | J Liu and B Rost (2002) Bioinformatics, 18, 922-933 |
| index - www-abstr-pdf | Inferring sub-cellular localization through automated lexical analysis | R Nair and B Rost (2002) Bioinformatics, 18:Suppl 1, S78-S86 |
| index - www-abstr-pdf | Loopy proteins appear conserved in evolution | J Liu, H Tan and B Rost (2002) J Mol Biol, 322, 53-64 |
| index - www-abstr-pdf | Sequence conserved for sub-cellular localization | R Nair and B Rost (2002) Protein Science, 11, 2836-2847 |
| index - www-abstr-pdf | Comparing function and structure between entire proteomes | J Liu and B Rost (2001) Protein Science, 10, 1970-1979 |
| Prediction services
|
| index - www-abstr | LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets | R Nair and B Rost (2004) Nucl Acids Res, volxx, |
| - | CHOP: parsing proteins into structural domains | J Liu and B Rost (2004) Nucl Acids Res, volxx, submitted |
| index - www-abstr | The PredictProtein server | B Rost, G Yachdav and J Liu (2004) Nucl Acids Res, volxx, in_press_pages |
| index - www-abstr-pdf | NORSp: predictions of long regions without regular secondary structure | J Liu and B Rost (2003) Nucl Acids Res, 31, 3833-3835 |
| index - www-abstr-pdf | LOC3D: annotate sub-cellular localization for protein structures | R Nair and B Rost (2003) Nucl Acids Res, 31, 3337-3340 |
| index - www-abstr-pdf | Static benchmarking of membrane helix predictions | A Kernytsky and B Rost (2003) Nucl Acids Res, 31, 3642-3644 |
| index - www-abstr-pdf | UniqueProt: creating sequence-unique protein data sets | S Mika and B Rost (2003) Nucl Acids Res, 31, 3789-3791 |
| index - www-abstr-pdf | META-PP: single crucial to prediction servers | VA Eyrich and B Rost (2003) Nucl Acids Res, 31, 3308-3310 |
| index - www-abstr-pdf | DSSPcont: continuous secondary structure assignments for proteins | P Carter, CAF Andersen and B Rost (2003) Nucl Acids Res, 31, 3293-3295 |
| index - www-abstr-pdf | EVA: evaluation of protein structure prediction servers | IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost (2003) Nucl Acids Res, 31, 3311-3315 |
| index - www-abstr-pdf | CAFASP3 in the spotlight of EVA | VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost (2003) Proteins, 53 S6, 548-560 |
| index - www-abstr-pdf | The PredictProtein server | B Rost and J Liu (2003) Nucl Acids Res, 31, 3300-3304 |
| index - www-abstr-pdf | PHD - an automatic server for protein secondary structure prediction | B Rost, C Sander and R Schneider (1994) CABIOS, 10, 53-60 |
| Sequence analysis
|
| index - www-abstr-pdf | Analysing six types of protein-protein interfaces | Y Ofran and B Rost (2003) J Mol Biol, 325, 377-387 |
| index - www-abstr-pdf | UniqueProt: creating sequence-unique protein data sets | S Mika and B Rost (2003) Nucl Acids Res, 31, 3789-3791 |
| index - www-abstr-pdf | META-PP: single crucial to prediction servers | VA Eyrich and B Rost (2003) Nucl Acids Res, 31, 3308-3310 |
| index - www-abstr-pdf | The PredictProtein server | B Rost and J Liu (2003) Nucl Acids Res, 31, 3300-3304 |
| index - www-abstr-pdf | Loopy proteins appear conserved in evolution | J Liu, H Tan and B Rost (2002) J Mol Biol, 322, 53-64 |
| index - www-abstr-pdf | Sequence conserved for sub-cellular localization | R Nair and B Rost (2002) Protein Science, 11, 2836-2847 |
| index - www-abstr-pdf | Comparing function and structure between entire proteomes | J Liu and B Rost (2001) Protein Science, 10, 1970-1979 |
| index - www-abstr-pdf | Twilight zone of protein sequence alignments | B Rost (1999) Protein Engineering, 12, 85-94 |
| index - www-abstr-pdf | The role of transmembrane domains in the functions of B- and T-cell receptors | R Zidovetzki, B Rost and I Pecht (1998) Immunology Letters, 64, 97-107 |
| index - www-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 and J Murken (1993) Nature Genetics, 5, 376-380 |
| Reviews
|
| index - www-abstr | Annotating protein function through lexical analysis | R Nair and B Rost (2004) AI Magazine, 25, 45-56 |
| - | How to use protein 1D structure predicted by PROFphd | B Rost (2004) in: 'Proteomics Handbook' (ed. JM Walker), Methods in Molecular Biology, Humana Press, submitted |
| index - www-abstr-pdf | Domains, motifs, and clusters in the protein universe | J Liu and B Rost (2003) Curr Opinion Chem Biol, 7, 5-11 |
| index - www-abstr | Secondary structure assignment | CAF Andersen and B Rost (2003) in: 'Structural Bioinformatics' (eds. P Bourne and H Weissig), New York: Wiley, 339-361 |
| index - www-abstr-pdf | Cataloguing proteins in cell cycle control | KO Wrzeszczynski and B Rost (2003) in: 'Cell cycle checkpoint control protocols' (ed. H Liebermann), Totowa: Humana Press, 219-233 |
| index - www-abstr | Prediction In 1D: secondary structure, membrane helices, and accessibility | B Rost (2003) in: 'Structural Bioinformatics' (eds. P Bourne and H Weissig), New York: Wiley, 557-585 |
| index - www-abstr | Rising accuracy of protein secondary structure prediction | B Rost (2003) in: 'Protein structure determination, analysis, and modeling for drug discovery' (ed. D Chasman), New York: Dekker, 207-249 |
| index - www-abstr-pdf | Neural networks predict protein structure: hype or hit? | B Rost (2003) in: 'Artificial intelligence and heuristic methods for bioinformatics' (ed. P Frasconi), Amsterdam: IOS Press, 34-50 |
| index - www-abstr-pdf | Prediction of protein structure through evolution | B Rost, J Liu, D Przybylski, R Nair, KO Wrzeszczynski, H Bigelow and Y Ofran (2003) in: 'Handbook of Chemoinformatics - From Data to Knowledge' (eds. J Gasteiger & T Engel), Weinheim: Wiley-VCH, 1789-1811 |
| index - www-abstr-pdf | Automatic prediction of protein function | B Rost, J Liu, R Nair, KO Wrzeszczynski and Y Ofran (2003) Cellular Molecular Life Sciences, 12, 2637-2650 |
| index - www-abstr-pdf | State-of-the-art in membrane protein prediction | CP Chen and B Rost (2002) Applied Bioinformatics, 1, 21-35 |
| index - www-abstr-pdf | Did evolution leap to create the protein universe? | B Rost (2002) Curr Opin Struc Biol, 12, 409-416 |
| index - www-abstr | Predict protein structure and function through evolutionary information | B Rost, J Liu, D Przybylski, R Nair, KO Wrzeszczynski, H Bigelow and Y Ofran (2002) New York: Columbia University, Preprint CUBIC_2002_12, Dec 2002 |
| index - www-abstr-pdf | Protein secondary structure prediction continues to rise | B Rost (2001) J Structural Biology, 134, 204-218 |
| index - www-abstr-pdf | EVA: large-scale analysis of secondary structure prediction | B Rost and VE Eyrich (2001) Proteins, 45:S5, S192-199 |
| index - www-abstr-pdf | Third generation prediction of secondary structure | B Rost and C Sander (2000) in: 'Protein structure prediction: Methods and Protocols' (ed. D. Webster), Totowa, NJ: Humana Press, 71-95 |
| index - www-abstr-pdf | Evolution teaches neural networks | B Rost (1999) in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau and ML Ristig), 207-223 |
| index - www-abstr | Neural networks for protein structure prediction: hype or hit? | B Rost (1999) |
| index - www-abstr | Pedestrian guide to analysing sequence databases | B Rost and R Schneider (1999) in: 'Core techniques in biochemistry' (eds. K Ashman), in press since 96.. |
| index - www-abstr-pdf | Protein structure prediction in 1D, 2D, and 3D | B Rost (1998) in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III and PR Schreiner), 3, 2242-2255 |
| index - www-abstr-pdf | Marrying structure and genomics | B Rost (1998) Structure, 6, 259-263 |
| index-abstr-pdf | NN which predicts protein secondary structure | B Rost (1997) in: 'Handbook of Neural Computation' (eds. E Fiesler and R Beale), G4.1 |
| index - www-abstr-pdf | Learning from evolution to predict protein structure | B Rost (1997) BCEC97: Bio-Computing and Emergent Computation, 87-101 |
| index - www-abstr-pdf | Sisyphus and prediction of protein structure | B Rost and SI O'Donoghue (1997) Computer Applications in Biological Science, 13, 345-356 |
| index - www | Sisyphus and protein structure prediction | B Rost (1997) 5th International Conference on Intelligent Systems for Molecular Biology, Tutorial |
| index-abstr-pdf | Bridging the protein sequence-structure gap by structure predictions | B Rost and C Sander (1996) Annual Review of Biophysics and Biomolecular Structure, 25, 113-136 |
| index - www-abstr-pdf | Pitfalls of protein sequence analysis | B Rost and A Valencia (1996) Current Opinion in Biotechnology, 7, 457-461 |
| index-abstr-pdf | Protein structure prediction by neural networks | B Rost and C Sander (1995) in: 'The handbook of brain theory and neural networks' (eds. M Arbib), 772-775 |
| index - www-abstr-pdf | Structure prediction of proteins - where are we now? | B Rost and C Sander (1994) Current Opinion in Biotechnology, 5, 372-380 |
| index - www-pdf | Neural networks in chemistry | B Rost and G Vriend (1993) CDA News, 8, 24-27 |
| index - www-abstr-pdf | Progress in protein structure prediction? | B Rost, C Sander and R Schneider (1993) TIBS, 18, 120-123 |
| Databases
|
| index - www-abstr | NLSdb: database of nuclear localization signals | R Nair, P Carter and B Rost (2003) Nucl Acid Res, 322, 397-399 |
| index - www-abstr-pdf | PEP: Predictions for Entire Proteomes | P Carter, J Liu and B Rost (2003) Nucl Acid Res, 31, 410-413 |
| index - www-abstr-pdf | LOC3D: annotate sub-cellular localization for protein structures | R Nair and B Rost (2003) Nucl Acids Res, 31, 3337-3340 |
| index - www-abstr-pdf | EVA: evaluation of protein structure prediction servers | IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost (2003) Nucl Acids Res, 31, 3311-3315 |
| index - www-abstr-pdf | CAFASP3 in the spotlight of EVA | VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost (2003) Proteins, 53 S6, 548-560 |
| index - www-abstr-pdf | Better prediction of sub-cellular localization through evolution and structure | R Nair and B Rost (2003) Proteins, 53, 917-930 |
| index - www-abstr-pdf | Finding nuclear localization signals | M Cokol, R Nair and B Rost (2000) EMBO Reports, 1, 411-415 |
| index - www-abstr-pdf | Twilight zone of protein sequence alignments | B Rost (1999) Protein Engineering, 12, 85-94 |
| index-abstr-pdf | TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures | B Rost (1995) Third International Conference on Intelligent Systems for Molecular Biology, 314-321 |