Protein conformational flexibility prediction using machine learning O Trott , K Siggers , B Rost , AG Palmer, 3rd J Magn Reson , 2008 , 192 :37-47 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 : 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 Predicting protein subcellular localization using intelligent systems R Nair , B Rost Methods Mol Biol , 2008 , 484 :435-463 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 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 : Secondary structure assignment CAF Andersen , B Rost Methods Biochem Anal. , 2008 , Secondary structure assignment :in press Natively unstructured regions in proteins identified from contact predictions A Schlessinger , M Punta , B Rost Bioinformatics , 2007 , 23 :2376-2384 Membrane protein prediction methods M Punta , LR Forrest , H Bigelow , A Kernytsky , J Liu , B Rost Methods , 2007 , 41 :460-474 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 Novel leverage of structural genomics J Liu , GT Montelione , B Rost Nature Biotechnology , 2007 , Novel leverage of structural genomics :in press ISMB/ECCB 2007 T Lengauer , B Rost , P Schuster Bioinformatics , 2007 , 23 :i1-i4 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 PROFbval: predict flexible and rigid residues in proteins A Schlessinger , G Yachdav , B Rost Bioinformatics , 2006 , 22 :891-893 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 Protein–protein interactions more conserved within species than across species S Mika , B Rost PLoS Computational Biology , 2006 , 2 :e79 PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow , B Rost Nucleic Acids Research , 2006 , 34 :W186-188 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 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 PROFcon: novel prediction of long-range contacts M Punta , B Rost Bioinformatics , 2005 , 21 :2960-2968 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 Mimicking cellular sorting improves prediction of subcellular localization R Nair , B Rost Journal of Molecular Biology , 2005 , 348 :85-100 NMPdb: database of nuclear matrix proteins S Mika , B Rost Nucleic Acids Research , 2005 , 33 :D160-163 EVAcon: a protein contact prediction evaluation service O Grana , VA Eyrich , F Pazos , B Rost , A Valencia Nucleic Acids Res , 2005 , 33 :W347-51 The transcriptional landscape of the mammalian genome P Carninci , et al. Science , 2005 , 309 :1559-1563 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 Annotating proteins from Endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes KO Wrzeszczynski , B Rost Cellular and Molecular Life Sciences , 2004 , 61 :1341-1353 Improving fold recognition without folds D Przybylski , B Rost Journal of Molecular Biology , 2004 , 341 :255-269 LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair , B Rost Nucleic Acids Research , 2004 , 32 :W517-W521 Protein names peeled precisely off free text S Mika , B Rost Bioinformatics , 2004 , 20 :I241-I247 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 AI and Bioinformatics J Glasgow , I Jurisica , B Rost AI Magazine , 2004 , 25 :7-8 Role of transmembrane domains in the functions of Fc receptors R Zidovetzki , B Rost , DL Armstrong , I Pecht Journal of Biophysical Chemistry , 2003 , 15 :555-575 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Prediction in 1D: secondary structure, membrane helices, and accessibility B Rost Methods Biochem Anal , 2003 , 44 :559-587 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 LOC3D: annotate sub-cellular localization for protein structures R Nair , B Rost Nucleic Acids Research , 2003 , 31 :3337-3340 UniqueProt: creating representative protein sequence sets S Mika , B Rost Nucleic Acids Research , 2003 , 31 :3789-3791 Domains, motifs, and clusters in the protein universe J Liu , B Rost Current Opinion in Chemical Biology , 2003 , 7 :5-11 Static benchmarking of membrane helix predictions A Kernytsky , B Rost Nucleic Acids Research , 2003 , 31 :3642-3644 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 DSSPcont: continuous secondary structure assignments for proteins P Carter , CAF Andersen , B Rost Nucleic Acids Research , 2003 , 31 :3293-3295 Automatic secondary structure assignment CAF Andersen , B Rost Methods Biochem Anal. , 2003 , 44 :341-363 Reply to Moult et al. A Sali , MA Marti-Renom , MS Madhusudhan , A Fiser , B Rost Structure , 2002 , 10 :292-293 Did evolution leap to create the protein universe? B Rost Current Opinion in Structural Biology , 2002 , 12 :409-416 Alignments grow, secondary structure prediction improves D Przybylski , B Rost Proteins: Structure, Function, and Bioinformatics , 2002 , 46 :195-205 Sequence conserved for sub-cellular localization R Nair , B Rost Protein Science , 2002 , 11 :2836-2847 Reliability of assessment of protein structure prediction methods MA Marti-Renom , MS Madhusudhan , A Fiser , B Rost , A Sali Structure , 2002 , 10 :435-440 Loopy proteins appear conserved in evolution J Liu , H Tan , B Rost Journal of Molecular Biology , 2002 , 322 :53-64 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 Protein secondary structure prediction continues to rise B Rost Journal of Structural Biology , 2001 , 134 :204-218 Comparing function and structure between entire proteomes J Liu , B Rost Protein Science , 2001 , 10 :1970-1979 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 Third generation prediction of secondary structure B Rost , C Sander Methods in Molecular Biology , 2000 , 143 :71-95 A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment A Zemla , C Venclovas , K Fidelis , B Rost Proteins: Structure, Function, and Genetics , 1999 , 34 :220-223 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 Effective use of sequence correlation and conservation in fold recognition O Olmea , B Rost , A Valencia Journal of Molecular Biology , 1999 , 293 :1221-1239 The role of transmembrane domains in the functions of B- and T-cell receptors R Zidovetzki , B Rost , I Pecht Immunology Letters , 1998 , 64 :97-107 Marrying structure and genomics B Rost Structure , 1998 , 6 :259-263 Sisyphus and prediction of protein structure B Rost , SI O'Donoghue Computer Applications in Biological Science , 1997 , 13 :345-356 Protein fold recognition by prediction-based threading B Rost , R Schneider , C Sander Journal of Molecular Biology , 1997 , 270 :471-480 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 Topology prediction for helical transmembrane proteins at 86% accuracy B Rost , R Casadio , P Fariselli Protein Science , 1996 , 5 :1704-1718 Pitfalls of protein sequence analysis B Rost , A Valencia Current Opinion in Biotechnology , 1996 , 7 :457-461 Bridging the protein sequence-structure gap by structure predictions B Rost , C Sander Annual Review of Biophysics and Biomolecular Structure , 1996 , 25 :113-136 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 Progress of 1D protein structure prediction at last B Rost , C Sander Proteins: Structure, Function, and Genetics , 1995 , 23 :295-300 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 Structure prediction of proteins - where are we now? B Rost , C Sander Current Opinion in Biotechnology , 1994 , 5 :372-380 PHD - an automatic server for protein secondary structure prediction B Rost , C Sander , R Schneider CABIOS , 1994 , 10 :53-60 Conservation and prediction of solvent accessibility in protein families B Rost , C Sander Proteins: Structure, Function, and Genetics , 1994 , 20 :216-226 1D secondary structure prediction through evolutionary profiles B Rost , C Sander in: 'Protein Structure by Distance Analysis ' (eds. H Bohr , S Brunak ), 1994 , : Amsterdam, Oxford, Washington 1D secondary structure prediction through evolutionary profiles :257-276 Secondary structure prediction of all-helical proteins in two states B Rost , C Sander Protein Engineering , 1993 , 6 :831-836 Prediction of protein secondary structure at better than 70% accuracy B Rost , C Sander Journal of Molecular Biology , 1993 , 232 :584-599 Improved prediction of protein secondary structure by use of sequence profiles and neural networks B Rost , C Sander Proceedings of the National Academy of Sciences , 1993 , 90 :7558-7562 Jury returns on structure prediction B Rost , C Sander Nature , 1992 , 360 :540 CUBIC: Results / Papers (by Year) Page index:  2008  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 Publications by Year 2008 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material NMR structure of the peptidyl-tRNA hydrolase domain from Pseudomonas syringae expands the structural coverage of the hydrolysis domains of class 1 peptide chain release factors KK Singarapu , R Xiao , T Acton , B Rost , GT Montelione , T Szyperski Proteins: Structure, Function, and Bioinformatics , 2008 , 71 :1027-1031 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 Powerful fusion: PSI-BLAST and consensus sequences D Przybylski , B Rost Bioinformatics , 2008 , Powerful fusion: PSI-BLAST and consensus sequences :in press ISMB 2008 Toronoto M Linial , JP Mesirov , B Morrison McKay , B Rost PLoS Computational Biology , 2008 , 4 :e1000094 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 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 2007 :  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 Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski , B Rost Nucleic Acids Research , 2007 , 35 :2238-2246 Prediction of DNA-binding residues from sequence Y Ofran , V Mysore , B Rost Bioinformatics , 2007 , 23 :i347-i353 Critical assessment of methods of protein structure prediction-Round VII J Moult , K Fidelis , A Kryshtafovych , B Rost , T Hubbard , A Tramontano Proteins , 2007 , 69 Suppl 8 :3-9 ISMB/ECCB 2007: The premier conference on computational biology T Lengauer , B Morrison McKay , B Rost PLoS Computational Biology , 2007 , 3 :e96 SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg , B Rost Nucleic Acids Research , 2007 , 35 :3823-3835 2006 :  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 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 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 Outcome of a workshop on archiving structural models of biological macromolecules HM Berman , et al. Structure , 2006 , 14 :1211-1217 2005 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Protein flexibility and rigidity predicted from sequence A Schlessinger , B Rost Proteins: Structure, Function, and Bioinformatics , 2005 , 61 :115-126 Protein folding rates estimated from contact predictions M Punta , B Rost Journal of Molecular Biology , 2005 , 348 :507-512 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 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 Critical assessment of methods of protein structure prediction (CASP)-Round 6 J Moult , K Fidelis , B Rost , T Hubbard , A Tramontano Proteins , 2005 , 61 :3-7 ISMB 2005 HV Jagadish , D States , B Rost Bioinformatics , 2005 , 21 Suppl 1 :i1-i2 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 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 2004 :  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 The PredictProtein server B Rost , G Yachdav , J Liu Nucleic Acids Research , 2004 , 32 :W321-W326 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 Annotating protein function through lexical analysis R Nair , B Rost AI Magazine , 2004 , 25 :45-56 NLProt: extracting protein names and sequences from papers S Mika , B Rost Nucleic Acids Research , 2004 , 32 :W634-W637 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 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 2003 :  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 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 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 Predict protein-protein interaction sites from local sequence information Y Ofran , B Rost FEBS Letters , 2003 , 544 :236-239 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 NORSp: predictions of long regions without regular secondary structure J Liu , B Rost Nucleic Acids Research , 2003 , 31 :3833-3835 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 META-PP: single interface to crucial prediction servers VA Eyrich , B Rost Nucleic Acids Research , 2003 , 31 :3308-3310 PEP: Predictions for Entire Proteomes P Carter , J Liu , B Rost Nucleic Acids Research , 2003 , 31 :410-413 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 2002 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology , 2002 , 318 :595-608 Bioinformatics in structural genomics B Rost , B Honig , A Valencia Bioinformatics , 2002 , 18 :897 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 Inferring sub-cellular localisation through automated lexical analysis R Nair , B Rost Bioinformatics , 2002 , 18 :S78-S86 Target space for structural genomics revisited J Liu , B Rost Bioinformatics , 2002 , 18 :922-933 Ismb 2002 J Glasgow , B Rost Bioinformatics , 2002 , 18 :S1 State-of-the-art in membrane prediction CP Chen , B Rost Applied Bioinformatics , 2002 , 1 :21-35 Continuum secondary structure captures protein flexibility CAF Andersen , AG Palmer , S Brunak , B Rost Structure , 2002 , 10 :175-184 2001 :  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 CAFASP2: the second critical assessment of fully automated structure prediction methods D Fischer , A Elofsson , L Rychlewski , F Pazos , A Valencia , B Rost , AR Ortiz , RLJ Dunbrack Proteins: Structure, Function, and Genetics , 2001 , 45 Suppl 5 :S171-S183 2000 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Finding nuclear localisation signals M Cokol , R Nair , B Rost EMBO Reports , 2000 , 1 :411-415 1999 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Twilight zone of protein sequence alignments B Rost Protein Engineering , 1999 , 12 :85-94 A platform for integrating threading results with protein family analyses F Pazos , B Rost , A Valencia Bioinformatics , 1999 , 15 :1062-1063 CAFASP-1: critical assessment of fully automated structure prediction methods D Fischer , C Barret , K Bryson , A Elofsson , A Godzik , D Jones , KJ Karplus , LA Kelley , RM MacCallum , K Pawowski , B Rost , L Rychlewski , M Sternberg Proteins: Structure, Function, and Genetics , 1999 , Suppl 3 :209-217 1998 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material 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 Adaptation of protein surfaces to subcellular location MA Andrade , SI O'Donoghue , B Rost Journal of Molecular Biology , 1998 , 276 :517-525 1997 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material 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 1996 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Refining neural network predictions for helical transmembrane proteins by dynamic programming B Rost , R Casadio , P Fariselli in: 'Fourth International Conference on Intelligent Systems for Molecular Biology ' (eds. D States , P Agarwal , T Gaasterland , L Hunter , RF Smith ), 1996 , : St. Louis, M.O., U.S.A. Refining neural network predictions for helical transmembrane proteins by dynamic programming :192-200 PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology , 1996 , 266 :525-539 Update on protein structure prediction: results of the 1995 IRBM workshop T Hubbard , et al. Folding & Design , 1996 , 1 :R55-R63 1995 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Protein structure prediction by neural networks B Rost , C Sander in: 'The handbook of brain theory and neural networks ' (eds. M Arbib ), 1995 , : Cambridge, MA Protein structure prediction by neural networks :772-775 Prediction of helical transmembrane segments at 95% accuracy B Rost , R Casadio , P Fariselli , C Sander Protein Science , 1995 , 4 :521-533 1994 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Redefining the goals of protein secondary structure prediction B Rost , C Sander , R Schneider Journal of Molecular Biology , 1994 , 235 :13-26 Evolution and neural networks - protein secondary structure prediction above 71% accuracy B Rost , C Sander , R Schneider in: '27th Hawaii International Conference on System Sciences ' (eds. L Hunter ), 1994 , 5 :385-394 Combining evolutionary information and neural networks to predict protein secondary structure B Rost , C Sander Proteins: Structure, Function, and Genetics , 1994 , 19 :55-72 Data based modeling of proteins L Holm , B Rost , C Sander , R Schneider , G Vriend in: 'Statistical Mechanics, Protein Structure, and Protein Substrate Interactions ' (eds. S Doniach ), 1994 , : New York Data based modeling of proteins :277-296 1993 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Progress in protein structure prediction? B Rost , C Sander , R Schneider Trends in Biochemical Sciences , 1993 , 18 :120-123 Neural networks in chemistry B Rost , G Vriend Chemical Design Autamation News , 1993 , 8 :24-27 Molecular modelling of the Norrie disease protein predicts a cysteine knot growth factor tertiary structure T Meitinger , A Meindl , P Bork , B Rost , C Sander , M Haasemann , J Murken Nature Genetics , 1993 , 5 :376-380 1992 :  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Exercising multi-layered networks on protein secondary structure B Rost , C Sander in: 'Neural Networks: From Biology to High Energy Physics ' (eds. O Benhar , S Brunak , P DelGiudice , M Grandolfo ), 1992 , 3 :209-220 Reprints & unpublished Documents: Surface profiles predict sub-cellular localisation R Nair and B Rost 2001 (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 (abstr, www, pdf) Neural networks for protein structure prediction: hype or hit? B Rost 1999 (abstr, www) Midnight zone of protein structure evolution Rost, S O'Donoghue and C Sander 1998 (abstr, www) Short yeast ORFs: expressed protein or not? B Rost 1999 (abstr, www) Pedestrian guide to analysing sequence databases. B Rost and R Schneider 1999 (abstr, www) Protein fold recognition by merging 1D structure prediction and sequence alignments B Rost 1996 (abstr, www) Sisyphus and protein structure prediction B Rost & SI O'Donoghue 1997 5th International Conference on Intelligent Systems for Molecular Biology, , Tutorial (abstr, www) WWW 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 Accuracy of predicting buried helices by PHDsec B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/PredBuriedHelices.html Appendix to 'Adaptation of protein surfaces to subcellular location' MA Andrade, SI O'Donoghue and B Rost 1998 http://cubic.bioc.columbia.edu/papers/ Appendix to 'Protein fold recognition by prediction-based threading' B Rost 1996 Appendix to 'Topology prediction for helical transmembrane proteins at 86% accuracy' B Rost 1996 Appendix to 'Twilight zone of protein sequence alignments' B Rost 1998 Average conservation of 1D structure between remote homologues B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/ConservationOf1D.html Expected prediction accuracy of PHD B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/ExpAccuracyPHD.html Observed secondary structure content for 721 proteins B Rost 1996 http://cubic.bioc.columbia.edu/~rost/Res/96/SecStrContent.html PredictProtein - internet prediction service B Rost 1997 http://cubic.bioc.columbia.edu/predictprotein/ WWW services for sequence analysis B Rost and R Schneider 1996 http://cubic.bioc.columbia.edu/