ROSTLAB - Results / Papers (by Year)

2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1996 1995 1994 1993 1992 Reprints & unpublished Web documents
Publication index - Sorted by category - Sorted by authors - Collected abstracts

2007: 123 abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family JM Aramini, YJ Huang, GV Swapna, JR Cort, PK Rajan, R Xiao, R Shastry, TB Acton, J Liu, B Rost, MA Kennedy, GT Montelione Proteins, 2007, 68:789-95 (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)
ISMB/ECCB 2007 T Lengauer, B Morrison McKay, B Rost Bioinformatics, 2007, 23:i1-i4 (pdf)
ISMB/ECCB 2007: The premier conference on computational biology T Lengauer, B Morrison McKay, B Rost PLoS Computational Biology, 2007, 3:e96 (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)
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)
Protein-protein interaction hot spots carved into sequences Y Ofran, B Rost PLoS Computational Biology, 2007, 3:e119 (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)
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)
Natively unstructured loops differ from other loops A Schlessinger, J Liu, B Rost PLoS Computational Biology, 2007, 3:e140 (abstr, web, som)
2006: 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)
Outcome of a workshop on archiving structural models of biological macromolecules HM Berman, et al. Structure, 2006, 14:1211-1217 (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)
Distinguishing protein-coding from non-coding RNAs through support vector machines. Liu J, Gough J, Rost B. 2006 PLoS Genet. 2006 Apr;2(4):e29. Epub 2006 Apr 28. (abstr, www, pdf)
PROFbval: predict flexible and rigid residues in proteins. Schlessinger A, Yachdav G, Rost B. 2006 Bioinformatics. 2006 Apr 1;22(7):891-3. Epub 2006 Feb 2. (abstr, www, pdf)
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Bigelow H, Rost B. 2006 Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W186-8. (abstr, www, pdf)
Protein Interactions in Disease: Session Introduction Maricel Kann, Yanay Ofran, Marco Punta and Predrag Radivojac 2006 Proceedings of the Pacific Symposium on Biocomputing 2006, 11:351-353 (abstr, www, pdf)
Protein-protein interactions more conserved within species than across species. Mika S, Rost B. 2006 PLoS Comput Biol. 2006 Jul 21;2(7):e79. Epub 2006 May 18. (abstr, www, pdf)
2005:
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery Y. Ofran, M. Punta, R. Schneider and B. Rost Drug Discov Today. 2005 10(21):1475-82 Review (abstr, www, pdf)
CASP6 assessment of contact prediction O. Grana, D. Baker, R.M. MacCallum, J. Meiler, M. Punta, B. Rost, M. L. Tress, and A. Valencia 2005 Proteins 2005 61 Suppl 7:214-24 (abstr, www, pdf)
Epitome: Database of structure-inferred antigenic epitopes A Schlessinger, Y Ofran, G Yachdav and B Rost 2005 NAR (Database Issue) 2005, in press. (abstr, www, pdf)
Mimicking cellular sorting improves prediction of Subcellular Localization. R Nair and B Rost 2005 Journal of Molecular Biology 2005 Apr 22;348(1):85-100. (abstr, www, pdf)
NMPdb: Database of Nuclear Matrix Proteins. S Mika and B Rost 2005 Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D160-3. (abstr, www, pdf)
PROFcon: novel prediction of long-range contacts M Punta and B Rost 2005 Bioinformatics, 2005, Jul 1;21(13):2960-8 (abstr, www, pdf)
Protein flexibility and rigidity predicted from sequence A Schlessinger and B Rost 2005 Proteins, 2005, in press (abstr, www, pdf)
Protein folding rates estimated from contact predictions M Punta and B Rost 2005 Journal of Molecular Biology Volume 348 (3), 507-512 (abstr, www, pdf)
2004:
AI and Bioinformatics J Glasgow, I Jurisica and B Rost 2004 AI Magazine, 25, 7-8 (abstr, www, pdf)
Annotating protein function through lexical analysis R Nair and B Rost 2004 AI Magazine, 25, 45-56 (abstr, www, pdf)
Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione and B Rost 2004 Proteins. 2004 Aug 1;56(2):188-200. (abstr, www, pdf)
CHOP proteins into structural domains J Liu and B Rost 2004 Proteins, 55, 678-686 (abstr, www, pdf)
CHOP: parsing proteins into structural domains J Liu and B Rost 2004 Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W569-W571. (abstr, www, pdf)
Improving fold recognition without folds D Przybylski and B Rost 2004 JMB, 2004 Jul30;341(1):255-69 (abstr, www, pdf)
LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair and B Rost 2004 Nucl. Acids. Res. 2004 32(Web Server Issue): W517-W521. (abstr, www, pdf)
NLProt: extracting protein names and sequences from papers S Mika and B Rost 2004 Nucleic Acids Res. 2004 32(Web Server issue):W634-W637; (abstr, www, pdf)
Predicting transmembrane beta-barrels for entire proteomes H Bigelow, D Petrey, J Liu, D Przybylski and B Rost 2004 NAR, 32, 2566-2577 (abstr, www, pdf)
Protein names precisely peeled off free text S Mika and B Rost 2004 Bioinformatics. 2004 Aug 4;20 Suppl 1:I241-I247; (abstr, www, pdf)
Sequence-based prediction of protein domains J Liu and B Rost 2004 Nucleic Acids Res. 2004 Jul 07;32(12):3522-30. Print 2004 (abstr, www, pdf)
The PredictProtein server B Rost, G Yachdav and J Liu 2004 Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W321-W326. (abstr, www, 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 and GT Montelione 2004 Proteins. 2004 Aug 1;56(2):181-187. (abstr, www, pdf)
2003:
Analysing six types of protein-protein interfaces Y Ofran and B Rost 2003 J Mol Biol, 325, 377-387 (abstr, www, 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 (abstr, www, pdf)
Better prediction of sub-cellular localization through evolution and structure R Nair and B Rost 2003 Proteins, 53, 917-930 (abstr, www, 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 (abstr, www, 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 (abstr, www, pdf)
DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen and B Rost 2003 Nucl Acids Res, 31, 3293-3295 (abstr, www, pdf)
Domains, motifs, and clusters in the protein universe J Liu and B Rost 2003 Curr Opinion Chem Biol, 7, 5-11 (abstr, www, 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 (abstr, www, pdf)
LOC3D: annotate sub-cellular localization for protein structures R Nair and B Rost 2003 Nucl Acids Res, 31, 3337-3340 (abstr, www, pdf)
Local sequence information can predict protein-protein interaction sites Y Ofran and B Rost 2003 FEBS Let, 544, 236-239 (abstr, www, pdf)
META-PP: single crucial to prediction servers VA Eyrich and B Rost 2003 Nucl Acids Res, 31, 3308-3310 (abstr, www, pdf)
NLSdb: database of nuclear localization signals R Nair, P Carter and B Rost 2003 Nucl Acid Res, 322, 397-399 (abstr, www, pdf)
NORSp: predictions of long regions without regular secondary structure J Liu and B Rost 2003 Nucl Acids Res, 31, 3833-3835 (abstr, www, 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 (abstr, www, pdf)
PEP: Predictions for Entire Proteomes P Carter, J Liu and B Rost 2003 Nucl Acid Res, 31, 410-413 (abstr, www, pdf)
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 (abstr, www, 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 (abstr, www, pdf)
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 (abstr, www, pdf)
Secondary structure assignment. CAF Andersen and B Rost 2003 in: 'Structural Bioinformatics' (eds P Bourne and H Weissig), New York: Wiley, 339-361 (abstr, www, 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 (abstr, www, pdf)
Static benchmarking of membrane helix predictions A Kernytsky and B Rost 2003 Nucl Acids Res, 31, 3642-3644 (abstr, www, pdf)
The PredictProtein server B Rost and J Liu 2003 Nucl Acids Res, 31, 3300-3304 (abstr, www, 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 (abstr, www, pdf)
UniqueProt: creating sequence-unique protein data sets S Mika and B Rost 2003 Nucl Acids Res, 31, 3789-3791 (abstr, www, pdf)
2002:
Alignments grow, secondary structure prediction improves D Przybylski and B Rost 2002 Proteins, 46, 197-205 (abstr, www, pdf)
Bioinformatics in structural genomics B Rost, B Honig and A Valencia 2002 Bioinformatics, 18, 897 (abstr, www, pdf)
Continuum secondary structure captures protein flexibility CAF Andersen, AG Palmer, S Brunak and B Rost 2002 Structure, 10, 175-185 (abstr, www, pdf)
Did evolution leap to create the protein universe? B Rost 2002 Curr Opin Struc Biol, 12, 409-416 (abstr, www, pdf)
Enzyme function less conserved than anticipated B Rost 2002 J Mol Biol, 318, 595-608 (abstr, www, pdf)
ISMB 2002 B Rost and J Glasgow 2002 Bioinformatics, 18:Suppl 1, S1 (abstr, 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 (abstr, www, pdf)
Inferring sub-cellular localization through automated lexical analysis R Nair and B Rost 2002 Bioinformatics, 18:Suppl 1, S78-S86 (abstr, www, pdf)
Long membrane helices and short loops predicted less accurately CP Chen and B Rost 2002 Protein Science, 11, 2766-2773 (abstr, www, pdf)
Loopy proteins appear conserved in evolution J Liu, H Tan and B Rost 2002 J Mol Biol, 322, 53-64 (abstr, 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 (abstr, www, pdf)
Sequence conserved for sub-cellular localization R Nair and B Rost 2002 Protein Science, 11, 2836-2847 (abstr, www, pdf)
State-of-the-art in membrane protein prediction CP Chen and B Rost 2002 Applied Bioinformatics, 1, 21-35 (abstr, www, pdf)
Target space for structural genomics revisited J Liu and B Rost 2002 Bioinformatics, 18, 922-933 (abstr, www, pdf)
Transmembrane helix predictions revisited CP Chen, A Kernytsky and B Rost 2002 Protein Science, 11, 2774-2791 (abstr, www, pdf)
2001:
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 (abstr, www, pdf)
Comparing function and structure between entire proteomes J Liu and B Rost 2001 Protein Science, 10, 1970-1979 (abstr, www, 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 (abstr, www, pdf)
EVA: large-scale analysis of secondary structure prediction B Rost and VE Eyrich 2001 Proteins, 45:S5, S192-199 (abstr, www, pdf)
Protein secondary structure prediction continues to rise B Rost 2001 J Structural Biology, 134, 204-218 (abstr, www, pdf)
2000:
Finding nuclear localization signals M Cokol, R Nair and B Rost 2000 EMBO Reports, 1, 411-415 (abstr, www, 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 (abstr, www, pdf)
1999:
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 (abstr, www, pdf)
A platform for integrating threading results with protein family analyses F Pazos, B Rost and A Valencia 1999 Bioinformatics, 15, 1062-1063 (abstr, www, 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 (abstr, www, pdf)
Evolution teaches neural networks. B Rost 1999 in: 'Scientific applications of neural nets' (eds JW Clark, T Lindenau and ML Ristig), , 207-223 (abstr, www, pdf)
Twilight zone of protein sequence alignments B Rost 1999 Protein Engineering, 12, 85-94 (abstr, www, pdf)
1998:
Adaptation of protein surfaces to subcellular location MA Andrade, SI O'Donoghue and B Rost 1998 Journal of Molecular Biology, 276, 517-525 (abstr, www, pdf)
Marrying structure and genomics B Rost 1998 Structure, 6, 259-263 (abstr, www, 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 (abstr, www, 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 (abstr, www, pdf)
1997:
Better 1D predictions by experts with machines. Proteins, Suppl B Rost 1997 1, 192-197 (abstr, www, pdf)
Learning from evolution to predict protein structure B Rost 1997 BCEC97: Bio-Computing and Emergent Computation, , 87-101 (abstr, www, pdf)
NN which predicts protein secondary structure. B Rost 1997 in: 'Handbook of Neural Computation' (eds E Fiesler and R Beale), , G4.1 (abstr, www, pdf)
Protein fold recognition by prediction-based threading B Rost, R Schneider and C Sander 1997 Journal of Molecular Biology, 270, 471-480 (abstr, www, pdf)
Protein structures sustain evolutionary drift B Rost 1997 Folding & Design, 2, S19-S24 (abstr, www, pdf)
Sisyphus and prediction of protein structure B Rost and SI O'Donoghue 1997 Computer Applications in Biological Science, 13, 345-356 (abstr, www, pdf)
1996:
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 (abstr, www, pdf)
PHD: predicting one-dimensional protein structure by profile based neural networks B Rost and A Valencia 1996 Current Opinion in Biotechnology, 7, 457-461 (abstr, www, pdf)
Pitfalls of protein sequence analysis B Rost and A Valencia 1996 Current Opinion in Biotechnology, 7, 457-461 (abstr, www, 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 (abstr, www, pdf)
Topology prediction for helical transmembrane proteins at 86% accuracy B Rost, R Casadio and P Fariselli 1996 Protein Science, 5, 1704-1718 (abstr, www, 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 Fjellstr?m, 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- (abstr, www, pdf)
1995:
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 (abstr, www, pdf)
Prediction of helical transmembrane segments at 95% accuracy B Rost, R Casadio, P Fariselli and C Sander 1995 Protein Science, 4, 521-533 (abstr, www, pdf)
Progress of 1D protein structure prediction at last B Rost and C Sander 1995 Proteins, 23, 295-300 (abstr, www, 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 (abstr, www, pdf)
TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost 1995 Third International Conference on Intelligent Systems for Molecular Biology, , 314-321 (abstr, www, pdf)
1994:
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 (abstr, www, pdf)
Combining evolutionary information and neural networks to predict protein secondary structure B Rost and C Sander 1994 Proteins, 19, 55-72 (abstr, www, pdf)
Conservation and prediction of solvent accessibility in protein families B Rost and C Sander 1994 Proteins, 20, 216-226 (abstr, www, pdf)
Data based modeling of proteins L Holm, B Rost, C Sander, R Schneider and G Vriend 1994 Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, , 277-296 (abstr, www, pdf)
Evolution and neural networks - protein secondary structure prediction above 71% accuracy B Rost, C Sander and R Schneider 1994 27th Hawaii International Conference on System Sciences, 5, 385-394 (abstr, www, pdf)
PHD - an automatic server for protein secondary structure prediction B Rost, C Sander and R Schneider 1994 CABIOS, 10, 53-60 (abstr, www, pdf)
Redefining the goals of protein secondary structure prediction B Rost, C Sander and R Schneider 1994 Journal of Molecular Biology, 235, 13-26 (abstr, www, pdf)
Structure prediction of proteins - where are we now? B Rost and C Sander 1994 Current Opinion in Biotechnology, 5, 372-380 (abstr, www, pdf)
1993:
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 (abstr, 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 (abstr, www, pdf)
Neural networks in chemistry B Rost and G Vriend 1993 CDA News, 8, 24-27 (abstr, www, pdf)
Prediction of protein secondary structure at better than 70% accuracy B Rost and C Sander 1993 Journal of Molecular Biology, 232, 584-599 (abstr, www, pdf)
Progress in protein structure prediction? B Rost, C Sander and R Schneider 1993 TIBS, 18, 120-123 (abstr, www, pdf)
Secondary structure prediction of all-helical proteins in two states B Rost and C Sander 1993 Protein Engineering, 6, 831-836 (abstr, www, pdf)
1992:
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 (abstr, www, pdf)
Jury returns on structure prediction B Rost and C Sander 1992 Nature, 360, 540 (abstr, www, pdf)
pending:
Annotating proteins from Endoplasmic Reticulum and Golgi apparatus in eukaryotic proteomes KO Wrzeszczynski and B Rost 2004 Cellular and Molecular Life Sciences, volxx, submitted_pages_xx (abstr, www, pdf)
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_pages_xx (abstr, www, pdf)
Predictive methods using protein sequence. Y Ofran and B Rost 2004 in: 'Bioinformatics' (eds AD Baxevanis & F Ouelette), Wiley, submitted_pages_xx (abstr, www, pdf)
Reprints and unpublished Documtents:
Midnight zone of protein structure evolution B Rost, S O'Donoghue and C Sander 1998 (abstr, www, pdf)
Neural networks for protein structure prediction: hype or hit? B Rost 1999 (abstr, www, pdf)
Pedestrian guide to analysing sequence databases. B Rost and R Schneider 1999 in: 'Core techniques in biochemistry' (eds K Ashman), , in press since 96... (abstr, www, pdf)
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 (abstr, www, pdf)
Protein fold recognition by merging 1D structure prediction and sequence alignments B Rost 1996 (abstr, www, pdf)
Short yeast ORFs: expressed protein or not? B Rost 1999 Preprint CUBIC, 1999_1 (abstr, www, 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 (abstr, www, pdf)
Sisyphus and protein structure prediction B Rost 1997 5th International Conference on Intelligent Systems for Molecular Biology, , Tutorial (abstr, www, pdf)
Surface profiles predict sub-cellular localisation R Nair and B Rost 2001 New York: Columbia University, Preprint CUBIC_2001_05, May 2001 (abstr, www, pdf)
WWW published Documents:
1D structure prediction for Chameleon (IgG binding domain of protein G) B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/PredChameleon.html (abstr, www, pdf)
Accuracy of predicting buried helices by PHDsec B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/PredBuriedHelices.html (abstr, www, pdf)
Appendix to 'Adaptation of protein surfaces to subcellular location' MA Andrade, SI O'Donoghue and B Rost 1998 http://cubic.bioc.columbia.edu/papers/ (abstr, www, pdf)
Appendix to 'Protein fold recognition by prediction-based threading' B Rost 1996 (abstr, www, pdf)
Appendix to 'Topology prediction for helical transmembrane proteins at 86% accuracy' B Rost 1996 (abstr, www, pdf)
Appendix to 'Twilight zone of protein sequence alignments' B Rost 1998 http://cubic.bioc.columbia.edu/papers/ (abstr, www, pdf)
Average conservation of 1D structure between remote homologues B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/ConservationOf1D.html (abstr, www, pdf)
Expected prediction accuracy of PHD B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/ExpAccuracyPHD.html (abstr, www, pdf)
Observed secondary structure content for 721 proteins B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/SecStrContent.html (abstr, www, pdf)
PredictProtein - internet prediction service B Rost 1997 http://cubic.bioc.columbia.edu/predictprotein/ (abstr, www, pdf)
WWW services for sequence analysis B Rost and R Schneider 1996 http://cubic.bioc.columbia.edu/ (abstr, www, pdf)