Secondary structure assignment CAF Andersen , B Rost Methods Biochem Anal. , 2008 , Secondary structure assignment :in press Automatic secondary structure assignment CAF Andersen , B Rost Methods Biochem Anal. , 2003 , 44 :341-363 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 ), 2008 , : Totowa, NJ Online tools for predicting integral membrane proteins : PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow , B Rost Nucleic Acids Research , 2006 , 34 :W186-188 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 , : Weinheim Prediction of protein structure through evolution :1789-1811 Comprehensive in silico mutagenesis highlights functionally improtant residues in proteins Y Bromberg , B Rost Bioinformatics , 2008 , Comprehensive in silico mutagenesis highlights functionally improtant residues in proteins :in press mlNODS: Split machine learning data sets using graphs Y Bromberg , B Rost CUBIC preprint, 2006 , : New York mlNODS: Split machine learning data sets using graphs :submitted 2006_03_20 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 PEP: Predictions for Entire Proteomes P Carter , J Liu , B Rost Nucleic Acids Research , 2003 , 31 :410-413 Transmembrane helix predictions revisited CP Chen , A Kernytsky , B Rost Protein Science , 2002 , 11 :2774-2791 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 Finding nuclear localisation signals M Cokol , R Nair , B Rost EMBO Reports , 2000 , 1 :411-415 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 EVA: continuous automatic evaluation of protein structure prediction servers V Eyrich , MA Martí-Renom , D Przybylski , A Fiser , F Pazos , A Valencia , A Sali , B Rost Bioinformatics , 2001 , 17 :1242-1243 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 Using genetic algorithms to select most predictive protein features A Kernytsky , B Rost Proteins: Structure, Function, and Bioinformatics , 2008 , Using genetic algorithms to select most predictive protein features :in press Static benchmarking of membrane helix predictions A Kernytsky , B Rost Nucleic Acids Research , 2003 , 31 :3642-3644 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 Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis JM Aramini , S Sharma , YJ Huang , GV Swapna , CK Ho , K Shetty , K Cunningham , LC Ma , L Zhao , LA Owens , M Jiang , R Xiao , J Liu , MC Baran , TB Acton , B Rost , GT Montelione Proteins: Structure, Function, and Genetics , 2008 , 72 :526-530 Membrane protein prediction methods M Punta , LR Forrest , H Bigelow , A Kernytsky , J Liu , B Rost Methods , 2007 , 41 :460-474 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 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 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 The PredictProtein server B Rost , G Yachdav , J Liu Nucleic Acids Research , 2004 , 32 :W321-W326 Sequence-based prediction of protein domains J Liu , B Rost Nucleic Acids Research , 2004 , 32 :3522-3530 CHOP proteins into structural domains J Liu , B Rost Proteins: Structure, Function, and Bioinformatics , 2004 , 55 :678-688 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 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 , : Weinheim Prediction of protein structure through evolution :1789-1811 NORSp: predictions of long regions without regular secondary structure J Liu , B Rost Nucleic Acids Research , 2003 , 31 :3833-3835 PEP: Predictions for Entire Proteomes P Carter , J Liu , B Rost Nucleic Acids Research , 2003 , 31 :410-413 Target space for structural genomics revisited J Liu , B Rost Bioinformatics , 2002 , 18 :922-933 Comparing function and structure between entire proteomes J Liu , B Rost Protein Science , 2001 , 10 :1970-1979 Protein–protein interactions more conserved within species than across species S Mika , B Rost PLoS Computational Biology , 2006 , 2 :e79 Protein names peeled precisely off free text S Mika , B Rost Bioinformatics , 2004 , 20 :I241-I247 UniqueProt: creating representative protein sequence sets S Mika , B Rost Nucleic Acids Research , 2003 , 31 :3789-3791 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 Predicting protein subcellular localization using intelligent systems R Nair , B Rost Methods Mol Biol , 2008 , 484 :435-463 Mimicking cellular sorting improves prediction of subcellular localization R Nair , B Rost Journal of Molecular Biology , 2005 , 348 :85-100 Annotating protein function through lexical analysis R Nair , B Rost AI Magazine , 2004 , 25 :45-56 Automatic prediction of protein function B Rost , J Liu , R Nair , KO Wrzeszczynski , Y Ofran Cellular and Molecular Life Sciences , 2003 , 60 :2637-2650 LOC3D: annotate sub-cellular localization for protein structures R Nair , B Rost Nucleic Acids Research , 2003 , 31 :3337-3340 Sequence conserved for sub-cellular localization R Nair , B Rost Protein Science , 2002 , 11 :2836-2847 Surface profiles predict sub-cellular localisation R Nair , B Rost CUBIC preprint, 2001 , Surface profiles predict sub-cellular localisation : Protein-protein interaction hot spots carved into sequences Y Ofran , B Rost PLoS Computational Biology , 2007 , 3 :e119 ISIS: Interaction Sites Identified from Sequence Y Ofran , B Rost Bioinformatics , 2007 , 23 :e13-16 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 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 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 , : Weinheim Prediction of protein structure through evolution :1789-1811 Predict protein-protein interaction sites from local sequence information Y Ofran , B Rost FEBS Letters , 2003 , 544 :236-239 Predicting simplified features of protein structure D Przybylski , B Rost in: 'Bioinformatics – From Genomes to Therapies ' (eds. T Lengauer ), 2008 , : Weinheim Predicting simplified features of protein structure :in press Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski , B Rost Nucleic Acids Research , 2007 , 35 :2238-2246 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 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 Alignments grow, secondary structure prediction improves D Przybylski , B Rost Proteins: Structure, Function, and Bioinformatics , 2002 , 46 :195-205 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 Building a neural network for predicting protein features M Punta , B Rost in: 'Application of Artificial Neural Networks to Chemistry and Biology ' (eds. D Livingston ), 2008 , : Totowa Building a neural network for predicting protein features :in press Membrane protein prediction methods M Punta , LR Forrest , H Bigelow , A Kernytsky , J Liu , B Rost Methods , 2007 , 41 :460-474 Protein folding rates estimated from contact predictions M Punta , B Rost Journal of Molecular Biology , 2005 , 348 :507-512 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 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 ), 2008 , Prediction of protein structure in 1D – Secondary structure, membrane regions, and solvent accessibility : How to use protein 1D structure predicted by PROFphd B Rost in: 'The Proteomics Protocols Handbook ' (eds. JE Walker ), 2005 , : Totowa NJ How 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 Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology , 2002 , 318 :595-608 Protein secondary structure prediction continues to rise B Rost Journal of Structural Biology , 2001 , 134 :204-218 Short yeast ORFs: expressed protein or not? B Rost CUBIC preprint, 1999 , Short yeast ORFs: expressed protein or not? : Evolution teaches neural networks B Rost in: 'Scientific applications of neural nets ' (eds. JW Clark , T Lindenau , ML Ristig ), 1999 , : Heidelberg Evolution teaches neural networks :207-223 Marrying structure and genomics B Rost Structure , 1998 , 6 :259-263 Learning from evolution to predict protein structure B Rost in: 'BCEC97: Bio-Computing and Emergent Computation ' (eds. B Olsson , D Lundh , A Narayanan ), 1997 , : Skövde, Sweden Learning from evolution to predict protein structure :87-101 Natively unstructured regions in proteins identified from contact predictions A Schlessinger , M Punta , B Rost Bioinformatics , 2007 , 23 :2376-2384 PROFbval: predict flexible and rigid residues in proteins A Schlessinger , G Yachdav , B Rost Bioinformatics , 2006 , 22 :891-893 Protein flexibility and rigidity predicted from sequence A Schlessinger , B Rost Proteins: Structure, Function, and Bioinformatics , 2005 , 61 :115-126 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 Loopy proteins appear conserved in evolution J Liu , H Tan , B Rost Journal of Molecular Biology , 2002 , 322 :53-64 Cataloguing proteins in cell cycle control KO Wrzeszczynski , B Rost Methods in Molecular Biology , 2004 , 241 :219-233 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 , : Weinheim Prediction of protein structure through evolution :1789-1811 PROFbval: predict flexible and rigid residues in proteins A Schlessinger , G Yachdav , B Rost Bioinformatics , 2006 , 22 :891-893 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 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 (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 Continuum secondary structure captures protein flexibility CAF Andersen , AG Palmer , S Brunak , B Rost Structure , 2002 , 10 :175-184 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 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 Y Bromberg (3):  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg , B Rost Nucleic Acids Research , 2007 , 35 :3823-3835 P Carter (4):  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material NLSdb: database of nuclear localization signals R Nair , P Carter , B Rost Nucleic Acids Research , 2003 , 31 :397-399 DSSPcont: continuous secondary structure assignments for proteins P Carter , CAF Andersen , B Rost Nucleic Acids Research , 2003 , 31 :3293-3295 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 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 H Hegyi (1):  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material A Kernytsky (4):  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 Transmembrane helix predictions revisited CP Chen , A Kernytsky , B Rost Protein Science , 2002 , 11 :2774-2791 IYY Koh (2):  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material CAFASP3 in the spotlight of EVA VA Eyrich , IYY Koh , D Przybylski , O Graña , F Pazos , A Valencia , B Rost Proteins: Structure, Function, and Bioinformatics , 2003 , 53 Suppl 6 :548-560 J Liu (27):  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 Novel leverage of structural genomics J Liu , GT Montelione , B Rost Nature Biotechnology , 2007 , Novel leverage of structural genomics :in press 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 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 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 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 CHOP: parsing proteins into structural domains J Liu , B Rost Nucleic Acids Research , 2004 , 32 :W569-W571 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Automatic prediction of protein function B Rost , J Liu , R Nair , KO Wrzeszczynski , Y Ofran Cellular and Molecular Life Sciences , 2003 , 60 :2637-2650 Domains, motifs, and clusters in the protein universe J Liu , B Rost Current Opinion in Chemical Biology , 2003 , 7 :5-11 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 Loopy proteins appear conserved in evolution J Liu , H Tan , B Rost Journal of Molecular Biology , 2002 , 322 :53-64 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 NLProt: extracting protein names and sequences from papers S Mika , B Rost Nucleic Acids Research , 2004 , 32 :W634-W637 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 LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair , B Rost Nucleic Acids Research , 2004 , 32 :W517-W521 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 , : Weinheim Prediction of protein structure through evolution :1789-1811 NLSdb: database of nuclear localization signals R Nair , P Carter , B Rost Nucleic Acids Research , 2003 , 31 :397-399 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 Inferring sub-cellular localisation through automated lexical analysis R Nair , B Rost Bioinformatics , 2002 , 18 :S78-S86 Finding nuclear localisation signals M Cokol , R Nair , B Rost EMBO Reports , 2000 , 1 :411-415 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 Epitome: Database of structure-inferred antigenic epitopes A Schlessinger , Y Ofran , G Yachdav , B Rost Nucleic Acids Research , 2006 , 34 :D777-780 Predictive methods using protein sequence Y Ofran , B Rost in: 'Bioinformatics ' (eds. AD Baxevanis , BF Ouellette ), 2005 , : New York Predictive methods using protein sequence :197-222 Rescue for statistical tests in high-throughput biology Y Ofran , B Rost CUBIC preprint, 2004 , : New York Rescue for statistical tests in high-throughput biology : Automatic prediction of protein function B Rost , J Liu , R Nair , KO Wrzeszczynski , Y Ofran Cellular and Molecular Life Sciences , 2003 , 60 :2637-2650 Analysing six types of protein-protein interfaces Y Ofran , B Rost Journal of Molecular Biology , 2003 , 325 :377-387 D Przybylski (12):  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Powerful fusion: PSI-BLAST and consensus sequences D Przybylski , B Rost Bioinformatics , 2008 , Powerful fusion: PSI-BLAST and consensus sequences :in press Improving fold recognition without folds D Przybylski , B Rost Journal of Molecular Biology , 2004 , 341 :255-269 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 , : Weinheim Prediction of protein structure through evolution :1789-1811 CAFASP3 in the spotlight of EVA VA Eyrich , IYY Koh , D Przybylski , O Graña , F Pazos , A Valencia , B Rost Proteins: Structure, Function, and Bioinformatics , 2003 , 53 Suppl 6 :548-560 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 EVA: continuous automatic evaluation of protein structure prediction servers V Eyrich , MA Martí-Renom , D Przybylski , A Fiser , F Pazos , A Valencia , A Sali , B Rost Bioinformatics , 2001 , 17 :1242-1243 M Punta (8):  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 , 23 :2376-2384 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 PROFcon: novel prediction of long-range contacts M Punta , B Rost Bioinformatics , 2005 , 21 :2960-2968 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 B Rost only single-author papers, here (21):  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Rising accuracy of protein secondary structure prediction B Rost in: 'Protein structure determination, analysis, and modeling for drug discovery ' (eds. D Chasman ), 2003 , : New York Rising accuracy of protein secondary structure prediction :207-249 Neural networks predict protein structure: hype or hit? B Rost in: 'Artificial intelligence and heuristic methods in bioinformatics ' (eds. P Frasconi , R Shamir ), 2003 , : Amsterdam Neural networks predict protein structure: hype or hit? :34-50 Did evolution leap to create the protein universe? B Rost Current Opinion in Structural Biology , 2002 , 12 :409-416 Twilight zone of protein sequence alignments B Rost Protein Engineering , 1999 , 12 :85-94 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 Protein structures sustain evolutionary drift B Rost Folding & Design , 1997 , 2 :S19-S24 NN which predicts protein secondary structure B Rost in: 'Handbook of Neural Computation ' (eds. E Fiesler , R Beale ), 1997 , : New York NN which predicts protein secondary structure :G4.1 Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics , 1997 , Suppl. 1 :192-197 PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology , 1996 , 266 :525-539 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, England TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures :314-321 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, Florida Fitting 1-D predictions into 3-D structures :132-151 Neural networks and evolution - advanced prediction of protein secondary structure B Rost Thesis, 1993 , Neural networks and evolution - advanced prediction of protein secondary structure : A Schlessinger (5):  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 Epitome: Database of structure-inferred antigenic epitopes A Schlessinger , Y Ofran , G Yachdav , B Rost Nucleic Acids Research , 2006 , 34 :D777-780 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 Annotating proteins from Endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes KO Wrzeszczynski , B Rost Cellular and Molecular Life Sciences , 2004 , 61 :1341-1353 Automatic prediction of protein function B Rost , J Liu , R Nair , KO Wrzeszczynski , Y Ofran Cellular and Molecular Life Sciences , 2003 , 60 :2637-2650 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 The PredictProtein server B Rost , G Yachdav , J Liu Nucleic Acids Research , 2004 , 32 :W321-W326