CUBIC Columbia University Bioinformatics

Automatic secondary structure assignment
CAF Andersen, B Rost
Methods Biochem Anal., 2003, 44:341-363 (abstr, web) Continuum secondary structure captures protein flexibility
CAF Andersen, AG Palmer, S Brunak, B Rost
Structure, 2002, 10:175-184 (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) 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) Prediction of protein structure through evolution
B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran
in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811 SNAP: predict effect of non-synonymous polymorphisms on function
Y Bromberg, B Rost
Nucleic Acids Research, 2007, 35:3823-3835 (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) PEP: Predictions for Entire Proteomes
P Carter, J Liu, B Rost
Nucleic Acids Research, 2003, 31:410-413 (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) Finding nuclear localisation signals
M Cokol, R Nair, B Rost
EMBO Reports, 2000, 1:411-415 (abstr, web, 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) 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) 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) Membrane protein prediction methods
M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost
Methods, 2007, 41:460-474 (pdf) Transmembrane helix predictions revisited
CP Chen, A Kernytsky, B Rost
Protein Science, 2002, 11:2774-2791 (abstr, web, 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) 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) Membrane protein prediction methods
M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost
Methods, 2007, 41:460-474 (pdf) Distinguishing protein-coding from non-coding RNA through support vector machines
J Liu, J Gough, B Rost
PLoS Genetics, 2006, 2:e29; DOI: 10.1371/journal.pgen.0020029 (abstr, web, pdf) 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) 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) 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) The PredictProtein server
B Rost, G Yachdav, J Liu
Nucleic Acids Research, 2004, 32:W321-W326 (abstr, web, 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) Domains, motifs, and clusters in the protein universe
J Liu, B Rost
Current Opinion in Chemical Biology, 2003, 7:5-11 (abstr, web, pdf) Automatic prediction of protein function
B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran
Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf) The PredictProtein server
B Rost, J Liu
Nucleic Acids Research, 2003, 31:3300-3304 (abstr, web, pdf) Target space for structural genomics revisited
J Liu, B Rost
Bioinformatics, 2002, 18:922-933 (abstr, web, pdf) Protein-protein interactions more conserved within species than across species
S Mika, B Rost
PLoS Computational Biology, 2006, 2:e79 (abstr, web, pdf, som) NLProt: extracting protein names and sequences from papers
S Mika, B Rost
Nucleic Acids Research, 2004, 32:W634-W637 (abstr, web, pdf) UniqueProt: creating representative protein sequence sets
S Mika, B Rost
Nucleic Acids Research, 2003, 31:3789-3791 (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) 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) Mimicking cellular sorting improves prediction of subcellular localization
R Nair, B Rost
Journal of Molecular Biology, 2005, 348:85-100 (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) LOC3D: annotate sub-cellular localization for protein structures
R Nair, B Rost
Nucleic Acids Research, 2003, 31:3337-3340 (abstr, web, pdf) Automatic prediction of protein function
B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran
Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf) Inferring sub-cellular localisation through automated lexical analysis
R Nair, B Rost
Bioinformatics, 2002, 18:S78-S86 (abstr, web, pdf) Surface profiles predict sub-cellular localisation
R Nair, B Rost
CUBIC preprint, 2001, Surface profiles predict sub-cellular localisation: (abstr, pdf) 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) Epitome: Database of structure-inferred antigenic epitopes
A Schlessinger, Y Ofran, G Yachdav, B Rost
Nucleic Acids Research, 2006, 34:D777-780 (abstr, web, pdf) Predictive methods using protein sequence
Y Ofran, B Rost
in: 'Bioinformatics' (eds. AD Baxevanis, BF Ouellette), 2005, : New YorkPredictive methods using protein sequence:197-222 (pdf) Analysing six types of protein-protein interfaces
Y Ofran, B Rost
Journal of Molecular Biology, 2003, 325:377-387 (abstr, web, pdf) Automatic prediction of protein function
B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran
Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf) 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) 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) Prediction of protein structure through evolution
B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran
in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811 Alignments grow, secondary structure prediction improves
D Przybylski, B Rost
Proteins: Structure, Function, and Bioinformatics, 2002, 46:195-205 (abstr, web, pdf) Simple jury predicts protein secondary structure best
B Rost, P Baldi, G Barton, J Cuff, V Eyrich, D Jones, K Karplus, R King, M Ouali, G Pollastri, D Przybylski
CUBIC preprint, 2001, Simple jury predicts protein secondary structure best:5 (abstr, web, pdf) Membrane protein prediction methods
M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost
Methods, 2007, 41:460-474 (pdf) Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks
A Passerini, M Punta, A Ceroni, B Rost, P Frasconi
Proteins: Structure, Function, and Bioinformatics, 2006, 65:305-316 (pdf) Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery
Y Ofran, M Punta, R Schneider, B Rost
Drug Discovery Today, 2005, 10:1475-1482 (pdf) Protein folding rates estimated from contact predictions
M Punta, B Rost
Journal of Molecular Biology, 2005, 348:507-512 (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 Prediction in 1D: secondary structure, membrane helices, and accessibility
B Rost
Methods Biochem Anal, 2003, 44:559-587 (abstr, web) Rising accuracy of protein secondary structure prediction
B Rost
in: 'Protein structure determination, analysis, and modeling for drug discovery' (eds. D Chasman), 2003, : New YorkRising accuracy of protein secondary structure prediction:207-249 (abstr, web) Did evolution leap to create the protein universe?
B Rost
Current Opinion in Structural Biology, 2002, 12:409-416 (abstr, web, pdf) Evolution teaches neural networks
B Rost
in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau, ML Ristig), 1999, : HeidelbergEvolution teaches neural networks:207-223 (abstr, web, pdf) Short yeast ORFs: expressed protein or not?
B Rost
CUBIC preprint, 1999, Short yeast ORFs: expressed protein or not?: (web) Marrying structure and genomics
B Rost
Structure, 1998, 6:259-263 (abstr, web, pdf) 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) Neural networks and evolution - advanced prediction of protein secondary structure
B Rost
Thesis, 1993, Neural networks and evolution - advanced prediction of protein secondary structure: Natively unstructured loops differ from other loops
A Schlessinger, J Liu, B Rost
PLoS Computational Biology, 2007, 3:e140 (abstr, web, som) 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) Protein flexibility and rigidity predicted from sequence
A Schlessinger, B Rost
Proteins: Structure, Function, and Bioinformatics, 2005, 61:115-126 (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) Loopy proteins appear conserved in evolution
J Liu, H Tan, B Rost
Journal of Molecular Biology, 2002, 322:53-64 (abstr, web, pdf) Annotating proteins from Endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes
KO Wrzeszczynski, B Rost
Cellular and Molecular Life Sciences, 2004, 61:1341-1353 (abstr, web) Automatic prediction of protein function
B Rost, J Liu, R Nair, KO Wrzeszczynski, Y Ofran
Cellular and Molecular Life Sciences, 2003, 60:2637-2650 (abstr, web, pdf) 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)

CUBIC: Results / Papers (by Author)
Page index: Andersen Bigelow Bromberg Carter Chen Cokol Eyrich Hegyi Kernytsky Koh Liu Mika Mozes Nair Ofran Przybylski Punta Rost Schlessinger Soong Tan Wrzeszczynski Yachdav
Publication index - Sorted by year - Sorted by category - Collected abstracts
Publications by Authors
CAF Andersen (3): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen, B Rost Nucleic Acids Research, 2003, 31:3293-3295 (abstr, web, pdf)
H Bigelow (5): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
Membrane protein prediction methods M Punta, LR Forrest, H Bigelow, A Kernytsky, J Liu, B Rost Methods, 2007, 41:460-474 (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)
Y Bromberg (2): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
mlNODS: Split machine learning data sets using graphs Y Bromberg, B Rost CUBIC preprint, 2006, : New YorkmlNODS: Split machine learning data sets using graphs:submitted 2006_03_20
P Carter (4): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
DSSPcont: continuous secondary structure assignments for proteins P Carter, CAF Andersen, B Rost Nucleic Acids Research, 2003, 31:3293-3295 (abstr, web, pdf)
NLSdb: database of nuclear localization signals R Nair, P Carter, B Rost Nucleic Acids Research, 2003, 31:397-399 (abstr, web)
CP Chen (3): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
State-of-the-art in membrane prediction CP Chen, B Rost Applied Bioinformatics, 2002, 1:21-35 (abstr, web, pdf)
M Cokol (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
V Eyrich (3): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
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)
H Hegyi (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
A Kernytsky (3): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
Static benchmarking of membrane helix predictions A Kernytsky, B Rost Nucleic Acids Research, 2003, 31:3642-3644 (abstr, web, pdf)
IYY Koh (2): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
EVA: evaluation of protein structure prediction servers IYY Koh, VA Eyrich, MA Marti-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Grana, A Valencia, A Sali, B Rost Nucleic Acids Research, 2003, 31:3311-3315 (abstr, web, pdf)
J Liu (26): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
Novel leverage of structural genomics J Liu, GT Montelione, B Rost Nature Biotechnology, 2007, Novel leverage of structural genomics:in press (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)
The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism J Benach, WC Edstrom, I Lee, K Das, B Cooper, R Xiao, J Liu, B Rost, TB Acton, GT Montelione, JF Hunt Acta Crystallogr D Biol Crystallogr, 2005, 61:589-98 (pdf)
Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination DA Snyder, Y Chen, NG Denissova, T Acton, JM Aramini, M Ciano, R Karlin, J Liu, P Manor, PA Rajan, P Rossi, GV Swapna, R Xiao, B Rost, J Hunt, GT Montelione J Am Chem Soc, 2005, 127:16505-11 (pdf)
Automatic target selection for structural genomics on eukaryotes J Liu, H Hegyi, TB Acton, GT Montelione, B Rost Proteins: Structure, Function, and Bioinformatics, 2004, 56:188-200 (abstr, web, pdf)
CHOP: parsing proteins into structural domains J Liu, B Rost Nucleic Acids Research, 2004, 32:W569-W571 (abstr, web, pdf)
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)
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)
PEP: Predictions for Entire Proteomes P Carter, J Liu, B Rost Nucleic Acids Research, 2003, 31:410-413 (abstr, web, pdf)
NORSp: predictions of long regions without regular secondary structure J Liu, B Rost Nucleic Acids Research, 2003, 31:3833-3835 (abstr, web, pdf)
Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811
Loopy proteins appear conserved in evolution J Liu, H Tan, B Rost Journal of Molecular Biology, 2002, 322:53-64 (abstr, web, pdf)
Comparing function and structure between entire proteomes J Liu, B Rost Protein Science, 2001, 10:1970-1979 (abstr, web, pdf)
S Mika (5): 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)
Protein names peeled precisely off free text S Mika, B Rost Bioinformatics, 2004, 20:I241-I247 (abstr, web, pdf)
E Mozes (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
R Nair (14): 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)
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)
NLSdb: database of nuclear localization signals R Nair, P Carter, B Rost Nucleic Acids Research, 2003, 31:397-399 (abstr, web)
Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811
Sequence conserved for sub-cellular localization R Nair, B Rost Protein Science, 2002, 11:2836-2847 (abstr, web, pdf)
Finding nuclear localisation signals M Cokol, R Nair, B Rost EMBO Reports, 2000, 1:411-415 (abstr, web, pdf)
Y Ofran (12): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
Prediction of DNA-binding residues from sequence Y Ofran, V Mysore, B Rost Bioinformatics, 2007, 23:i347-i353 (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)
Beyond annotation transfer by homology: novel protein function prediction methods that can assist drug discovery Y Ofran, M Punta, R Schneider, B Rost Drug Discovery Today, 2005, 10:1475-1482 (pdf)
Rescue for statistical tests in high-throughput biology Y Ofran, B Rost CUBIC preprint, 2004, : New YorkRescue for statistical tests in high-throughput biology:
Predict protein-protein interaction sites from local sequence information Y Ofran, B Rost FEBS Letters, 2003, 544:236-239 (abstr, web, pdf)
Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811
D Przybylski (11): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
Predicting simplified features of protein structure D Przybylski, B Rost in: 'Bioinformatics - From Genomes to Therapies' (eds. T Lengauer), 2007, : WeinheimPredicting simplified features of protein structure:in press (abstr, web)
Improving fold recognition without folds D Przybylski, B Rost Journal of Molecular Biology, 2004, 341:255-269 (abstr, web, pdf)
EVA: evaluation of protein structure prediction servers IYY Koh, VA Eyrich, MA Marti-Renom, D Przybylski, MS Madhusudhan, E Narayanan, O Grana, A Valencia, A Sali, B Rost Nucleic Acids Research, 2003, 31:3311-3315 (abstr, web, pdf)
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles G Pollastri, D Przybylski, B Rost, P Baldi Proteins: Structure, Function, and Bioinformatics, 2002, 47:228-235 (pdf)
EVA: 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)
M Punta (7): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
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)
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)
PROFcon: novel prediction of long-range contacts M Punta, B Rost Bioinformatics, 2005, 21:2960-2968 (abstr, web, pdf)
B Rost only single-author papers, here (21): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
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)
Neural networks predict protein structure: hype or hit? B Rost in: 'Artificial intelligence and heuristic methods in bioinformatics' (eds. P Frasconi, R Shamir), 2003, : AmsterdamNeural networks predict protein structure: hype or hit?:34-50 (abstr, web, pdf)
Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology, 2002, 318:595-608 (abstr, web, pdf)
Protein secondary structure prediction continues to rise B Rost Journal of Structural Biology, 2001, 134:204-218 (abstr, web, pdf)
Twilight zone of protein sequence alignments B Rost Protein Engineering, 1999, 12:85-94 (abstr, web, pdf)
Protein structure prediction in 1D, 2D, and 3D B Rost in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III, PR Schreiner), 1998, 3:2242-2255 (abstr, web, pdf)
Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics, 1997, Suppl. 1:192-197 (abstr, web, pdf)
NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation' (eds. E Fiesler, R Beale), 1997, : New YorkNN which predicts protein secondary structure:G4.1 (abstr, pdf)
Protein structures sustain evolutionary drift B Rost Folding & Design, 1997, 2:S19-S24 (abstr, web, pdf)
Fitting 1-D predictions into 3-D structures B Rost in: 'Protein folds: a distance based approach' (eds. H Bohr, S Brunak, S Brunak), 1995, : Boca Raton, FloridaFitting 1-D predictions into 3-D structures:132-151 (abstr, pdf)
TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures B Rost in: 'Third International Conference on Intelligent Systems for Molecular Biology' (eds. C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, S Wodak), 1995, : Cambridge, EnglandTOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures:314-321 (abstr, pdf)
A Schlessinger (5): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
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)
T-T Soong (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
H Tan (1): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
KO Wrzeszczynski (4): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
Cataloguing proteins in cell cycle control KO Wrzeszczynski, B Rost Methods in Molecular Biology, 2004, 241:219-233 (abstr, web, pdf)
Prediction of protein structure through evolution B Rost, J Liu, D Przybylski, R Nair, H Bigelow, KO Wrzeszczynski, Y Ofran in: 'Handbook of Chemoinformatics - from data to knowledge' (eds. J Gasteiger, T Engel), 2003, : WeinheimPrediction of protein structure through evolution:1789-1811
G Yachdav (4): abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material
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 PredictProtein server B Rost, G Yachdav, J Liu Nucleic Acids Research, 2004, 32:W321-W326 (abstr, web, pdf)