Powerful fusion: PSI-BLAST and consensus sequences D Przybylski , B Rost Bioinformatics , 2008 , Powerful fusion: PSI-BLAST and consensus sequences :in press Powerful fusion: PSI-BLAST and consensus sequences D Przybylski , B Rost Bioinformatics , 2008 , Powerful fusion: PSI-BLAST and consensus sequences :in press Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski , B Rost Nucleic Acids Research , 2007 , 35 :2238-2246 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 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 Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology , 2002 , 318 :595-608 Alignments grow, secondary structure prediction improves D Przybylski , B Rost Proteins: Structure, Function, and Bioinformatics , 2002 , 46 :195-205 Twilight zone of protein sequence alignments B Rost Protein Engineering , 1999 , 12 :85-94 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 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 in protein structure prediction? B Rost , C Sander , R Schneider Trends in Biochemical Sciences , 1993 , 18 :120-123 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 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 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 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 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 Better 1D predictions by experts with machines B Rost Proteins: Structure, Function, and Genetics , 1997 , Suppl. 1 :192-197 Powerful fusion: PSI-BLAST and consensus sequences D Przybylski , B Rost Bioinformatics , 2008 , Powerful fusion: PSI-BLAST and consensus sequences :in press Novel leverage of structural genomics J Liu , GT Montelione , B Rost Nature Biotechnology , 2007 , Novel leverage of structural genomics :in press Improving fold recognition without folds D Przybylski , B Rost Journal of Molecular Biology , 2004 , 341 :255-269 CHOP: parsing proteins into structural domains J Liu , B Rost Nucleic Acids Research , 2004 , 32 :W569-W571 CHOP proteins into structural domains J Liu , B Rost Proteins: Structure, Function, and Bioinformatics , 2004 , 55 :678-688 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 Domains, motifs, and clusters in the protein universe J Liu , B Rost Current Opinion in Chemical Biology , 2003 , 7 :5-11 Novel leverage of structural genomics J Liu , GT Montelione , B Rost Nature Biotechnology , 2007 , Novel leverage of structural genomics :in press Improving fold recognition without folds D Przybylski , B Rost Journal of Molecular Biology , 2004 , 341 :255-269 Reliability of assessment of protein structure prediction methods MA Marti-Renom , MS Madhusudhan , A Fiser , B Rost , A Sali Structure , 2002 , 10 :435-440 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 Powerful fusion: PSI-BLAST and consensus sequences D Przybylski , B Rost Bioinformatics , 2008 , Powerful fusion: PSI-BLAST and consensus sequences :in press 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 NMPdb: database of nuclear matrix proteins S Mika , B Rost Nucleic Acids Research , 2005 , 33 :D160-163 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 PEP: Predictions for Entire Proteomes P Carter , J Liu , B Rost Nucleic Acids Research , 2003 , 31 :410-413 Marrying structure and genomics B Rost Structure , 1998 , 6 :259-263 Natively unstructured regions in proteins identified from contact predictions A Schlessinger , M Punta , B Rost Bioinformatics , 2007 , 23 :2376-2384 Natively unstructured loops differ from other loops A Schlessinger , J Liu , B Rost PLoS Computational Biology , 2007 , 3 :e140 Natively unstructured loops differ from other loops A Schlessinger , J Liu , B Rost PLoS Computational Biology , 2007 , 3 :e140 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 Loopy proteins appear conserved in evolution J Liu , H Tan , B Rost Journal of Molecular Biology , 2002 , 322 :53-64 ISMB 2008 Toronoto M Linial , JP Mesirov , B Morrison McKay , B Rost PLoS Computational Biology , 2008 , 4 :e1000094 ISMB/ECCB 2007 T Lengauer , B Rost , P Schuster Bioinformatics , 2007 , 23 :i1-i4 ISMB 2005 HV Jagadish , D States , B Rost Bioinformatics , 2005 , 21 Suppl 1 :i1-i2 AI and Bioinformatics J Glasgow , I Jurisica , B Rost AI Magazine , 2004 , 25 :7-8 Ismb 2002 J Glasgow , B Rost Bioinformatics , 2002 , 18 :S1 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 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 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 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 PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Enzyme function less conserved than anticipated B Rost Journal of Molecular Biology , 2002 , 318 :595-608 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 EVA: large-scale analysis of secondary structure prediction B Rost , V Eyrich Proteins: Structure, Function, and Genetics , 2001 , 45 Suppl 5 :S192-S199 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 Protein fold recognition by prediction-based threading B Rost , R Schneider , C Sander Journal of Molecular Biology , 1997 , 270 :471-480 Progress of 1D protein structure prediction at last B Rost , C Sander Proteins: Structure, Function, and Genetics , 1995 , 23 :295-300 Natively unstructured regions in proteins identified from contact predictions A Schlessinger , M Punta , B Rost Bioinformatics , 2007 , 23 :2376-2384 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 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 Protein–protein interactions more conserved within species than across species S Mika , B Rost PLoS Computational Biology , 2006 , 2 :e79 PROFcon: novel prediction of long-range contacts M Punta , B Rost Bioinformatics , 2005 , 21 :2960-2968 LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair , B Rost Nucleic Acids Research , 2004 , 32 :W517-W521 Sequence-based prediction of protein domains J Liu , B Rost Nucleic Acids Research , 2004 , 32 :3522-3530 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 Sequence conserved for sub-cellular localization R Nair , B Rost Protein Science , 2002 , 11 :2836-2847 Topology prediction for helical transmembrane proteins at 86% accuracy B Rost , R Casadio , P Fariselli Protein Science , 1996 , 5 :1704-1718 Combining evolutionary information and neural networks to predict protein secondary structure B Rost , C Sander Proteins: Structure, Function, and Genetics , 1994 , 19 :55-72 Prediction of protein secondary structure at better than 70% accuracy B Rost , C Sander Journal of Molecular Biology , 1993 , 232 :584-599 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 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 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 Protein conformational flexibility prediction using machine learning O Trott , K Siggers , B Rost , AG Palmer, 3rd J Magn Reson , 2008 , 192 :37-47 PROFbval: predict flexible and rigid residues in proteins A Schlessinger , G Yachdav , B Rost Bioinformatics , 2006 , 22 :891-893 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Automatic secondary structure assignment CAF Andersen , B Rost Methods Biochem Anal. , 2003 , 44 :341-363 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 Secondary structure assignment CAF Andersen , B Rost Methods Biochem Anal. , 2008 , Secondary structure assignment :in press 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 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 LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets R Nair , B Rost Nucleic Acids Research , 2004 , 32 :W517-W521 Sequence-based prediction of protein domains J Liu , B Rost Nucleic Acids Research , 2004 , 32 :3522-3530 CHOP: parsing proteins into structural domains J Liu , B Rost Nucleic Acids Research , 2004 , 32 :W569-W571 CHOP proteins into structural domains J Liu , B Rost Proteins: Structure, Function, and Bioinformatics , 2004 , 55 :678-688 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 Prediction in 1D: secondary structure, membrane helices, and accessibility B Rost Methods Biochem Anal , 2003 , 44 :559-587 Automatic secondary structure assignment CAF Andersen , B Rost Methods Biochem Anal. , 2003 , 44 :341-363 Comparing function and structure between entire proteomes J Liu , B Rost Protein Science , 2001 , 10 :1970-1979 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 : 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 : 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 : 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 : 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 : 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 : Membrane protein prediction methods M Punta , LR Forrest , H Bigelow , A Kernytsky , J Liu , B Rost Methods , 2007 , 41 :460-474 Membrane protein prediction methods M Punta , LR Forrest , H Bigelow , A Kernytsky , J Liu , B Rost Methods , 2007 , 41 :460-474 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 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 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 PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow , B Rost Nucleic Acids Research , 2006 , 34 :W186-188 PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow , B Rost Nucleic Acids Research , 2006 , 34 :W186-188 PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow , B Rost Nucleic Acids Research , 2006 , 34 :W186-188 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 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 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 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 transmembrane beta-barrels for entire proteomes H Bigelow , D Petrey , J Liu , D Przybylski , B Rost Nucleic Acids Research , 2004 , 32 :2566-2577 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Target space for structural genomics revisited J Liu , B Rost Bioinformatics , 2002 , 18 :922-933 Transmembrane helix predictions revisited CP Chen , A Kernytsky , B Rost Protein Science , 2002 , 11 :2774-2791 State-of-the-art in membrane prediction CP Chen , B Rost Applied Bioinformatics , 2002 , 1 :21-35 State-of-the-art in membrane prediction CP Chen , B Rost Applied Bioinformatics , 2002 , 1 :21-35 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 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 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 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 Topology prediction for helical transmembrane proteins at 86% accuracy B Rost , R Casadio , P Fariselli Protein Science , 1996 , 5 :1704-1718 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 Prediction of helical transmembrane segments at 95% accuracy B Rost , R Casadio , P Fariselli , C Sander Protein Science , 1995 , 4 :521-533 Prediction of helical transmembrane segments at 95% accuracy B Rost , R Casadio , P Fariselli , C Sander Protein Science , 1995 , 4 :521-533 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 Powerful fusion: PSI-BLAST and consensus sequences D Przybylski , B Rost Bioinformatics , 2008 , Powerful fusion: PSI-BLAST and consensus sequences :in press 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 ISIS: Interaction Sites Identified from Sequence Y Ofran , B Rost Bioinformatics , 2007 , 23 :e13-16 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 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 EVAcon: a protein contact prediction evaluation service O Grana , VA Eyrich , F Pazos , B Rost , A Valencia Nucleic Acids Res , 2005 , 33 :W347-51 Improving fold recognition without folds D Przybylski , B Rost Journal of Molecular Biology , 2004 , 341 :255-269 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 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 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 The transcriptional landscape of the mammalian genome P Carninci , et al. Science , 2005 , 309 :1559-1563 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 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 SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg , B Rost Nucleic Acids Research , 2007 , 35 :3823-3835 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 PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow , B Rost Nucleic Acids Research , 2006 , 34 :W186-188 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 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 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 LOC3D: annotate sub-cellular localization for protein structures R Nair , B Rost Nucleic Acids Research , 2003 , 31 :3337-3340 NORSp: predictions of long regions without regular secondary structure J Liu , B Rost Nucleic Acids Research , 2003 , 31 :3833-3835 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 ISIS: Interaction Sites Identified from Sequence Y Ofran , B Rost Bioinformatics , 2007 , 23 :e13-16 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 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Analysing six types of protein-protein interfaces Y Ofran , B Rost Journal of Molecular Biology , 2003 , 325 :377-387 CUBIC: Results / Papers (by Category) Page index:   Alignment methods   CASP   Clustering proteins   Comparative modelling   Databases   Disorder   Editorial   Evaluation of prediction methods   Evolution   Experimental structure   Flexibility   Genomics predictions   Membrane regions   Methods   Non-coding RNA   Prediction services   Protein binding   Protein function   Protein structure   Protein-protein interaction   Protemic predictions   Reviews   Secondary structure   Sequence analysis   Solvent accessibility   Structural genomics   Subcellular localization   Threading (remote homology) Publication index - Sorted by year - Sorted by authors - Collected abstracts Publications by Category (topic/keyword) Alignment methods:  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 Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski , B Rost Nucleic Acids Research , 2007 , 35 :2238-2246 Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski , B Rost Nucleic Acids Research , 2007 , 35 :2238-2246 Improving fold recognition without folds D Przybylski , B Rost Journal of Molecular Biology , 2004 , 341 :255-269 CHOP proteins into structural domains J Liu , B Rost Proteins: Structure, Function, and Bioinformatics , 2004 , 55 :678-688 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Alignments grow, secondary structure prediction improves D Przybylski , B Rost Proteins: Structure, Function, and Bioinformatics , 2002 , 46 :195-205 Twilight zone of protein sequence alignments B Rost Protein Engineering , 1999 , 12 :85-94 Topology prediction for helical transmembrane proteins at 86% accuracy B Rost , R Casadio , P Fariselli Protein Science , 1996 , 5 :1704-1718 PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology , 1996 , 266 :525-539 Combining evolutionary information and neural networks to predict protein secondary structure B Rost , C Sander Proteins: Structure, Function, and Genetics , 1994 , 19 :55-72 Prediction of protein secondary structure at better than 70% accuracy B Rost , C Sander Journal of Molecular Biology , 1993 , 232 :584-599 CASP:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material 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 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 EVA: large-scale analysis of secondary structure prediction B Rost , V Eyrich Proteins: Structure, Function, and Genetics , 2001 , 45 Suppl 5 :S192-S199 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 Clustering proteins:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski , B Rost Nucleic Acids Research , 2007 , 35 :2238-2246 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 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 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 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 Domains, motifs, and clusters in the protein universe J Liu , B Rost Current Opinion in Chemical Biology , 2003 , 7 :5-11 Comparative modelling:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Outcome of a workshop on archiving structural models of biological macromolecules HM Berman , et al. Structure , 2006 , 14 :1211-1217 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 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 Databases:  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 Epitome: Database of structure-inferred antigenic epitopes A Schlessinger , Y Ofran , G Yachdav , B Rost Nucleic Acids Research , 2006 , 34 :D777-780 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 NLSdb: database of nuclear localization signals R Nair , P Carter , B Rost Nucleic Acids Research , 2003 , 31 :397-399 Twilight zone of protein sequence alignments B Rost Protein Engineering , 1999 , 12 :85-94 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 Disorder:  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 Natively unstructured loops differ from other loops A Schlessinger , J Liu , B Rost PLoS Computational Biology , 2007 , 3 :e140 PROFbval: predict flexible and rigid residues in proteins A Schlessinger , G Yachdav , B Rost Bioinformatics , 2006 , 22 :891-893 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Editorial:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material ISMB/ECCB 2007: The premier conference on computational biology T Lengauer , B Morrison McKay , B Rost PLoS Computational Biology , 2007 , 3 :e96 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 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 Bioinformatics in structural genomics B Rost , B Honig , A Valencia Bioinformatics , 2002 , 18 :897 Evaluation of prediction methods:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Predicting protein subcellular localization using intelligent systems R Nair , B Rost Methods Mol Biol , 2008 , 484 :435-463 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 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 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 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 Reliability of assessment of protein structure prediction methods MA Marti-Renom , MS Madhusudhan , A Fiser , B Rost , A Sali Structure , 2002 , 10 :435-440 State-of-the-art in membrane prediction CP Chen , B Rost Applied Bioinformatics , 2002 , 1 :21-35 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 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 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 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 Redefining the goals of protein secondary structure prediction B Rost , C Sander , R Schneider Journal of Molecular Biology , 1994 , 235 :13-26 Evolution:  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 Prediction of DNA-binding residues from sequence Y Ofran , V Mysore , B Rost Bioinformatics , 2007 , 23 :i347-i353 SNAP: predict effect of non-synonymous polymorphisms on function Y Bromberg , B Rost Nucleic Acids Research , 2007 , 35 :3823-3835 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 Protein–protein interactions more conserved within species than across species S Mika , B Rost PLoS Computational Biology , 2006 , 2 :e79 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 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 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 Protein structures sustain evolutionary drift B Rost Folding & Design , 1997 , 2 :S19-S24 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 Progress in protein structure prediction? B Rost , C Sander , R Schneider Trends in Biochemical Sciences , 1993 , 18 :120-123 Experimental structure:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material 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 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 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 Flexibility:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Secondary structure assignment CAF Andersen , B Rost Methods Biochem Anal. , 2008 , Secondary structure assignment :in press PROFbval: predict flexible and rigid residues in proteins A Schlessinger , G Yachdav , B Rost Bioinformatics , 2006 , 22 :891-893 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 Genomics predictions:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material 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 Novel leverage of structural genomics J Liu , GT Montelione , B Rost Nature Biotechnology , 2007 , Novel leverage of structural genomics :in press 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 transcriptional landscape of the mammalian genome P Carninci , et al. Science , 2005 , 309 :1559-1563 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 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 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 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 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 Target space for structural genomics revisited J Liu , B Rost Bioinformatics , 2002 , 18 :922-933 Marrying structure and genomics B Rost Structure , 1998 , 6 :259-263 Membrane regions:  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 ), 2008 , Prediction of protein structure in 1D – Secondary structure, membrane regions, and solvent accessibility : 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 : 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 : 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 : 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 : Membrane protein prediction methods M Punta , LR Forrest , H Bigelow , A Kernytsky , J Liu , B Rost Methods , 2007 , 41 :460-474 Membrane protein prediction methods M Punta , LR Forrest , H Bigelow , A Kernytsky , J Liu , B Rost Methods , 2007 , 41 :460-474 Membrane protein prediction methods M Punta , LR Forrest , H Bigelow , A Kernytsky , J Liu , B Rost Methods , 2007 , 41 :460-474 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 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 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 PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow , B Rost Nucleic Acids Research , 2006 , 34 :W186-188 PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins H Bigelow , B Rost Nucleic Acids Research , 2006 , 34 :W186-188 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 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 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 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 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 transmembrane beta-barrels for entire proteomes H Bigelow , D Petrey , J Liu , D Przybylski , B Rost Nucleic Acids Research , 2004 , 32 :2566-2577 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Transmembrane helix predictions revisited CP Chen , A Kernytsky , B Rost Protein Science , 2002 , 11 :2774-2791 Transmembrane helix predictions revisited CP Chen , A Kernytsky , B Rost Protein Science , 2002 , 11 :2774-2791 State-of-the-art in membrane prediction CP Chen , B Rost Applied Bioinformatics , 2002 , 1 :21-35 State-of-the-art in membrane prediction CP Chen , B Rost Applied Bioinformatics , 2002 , 1 :21-35 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 Comparing function and structure between entire proteomes J Liu , B Rost Protein Science , 2001 , 10 :1970-1979 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 Topology prediction for helical transmembrane proteins at 86% accuracy B Rost , R Casadio , P Fariselli Protein Science , 1996 , 5 :1704-1718 Topology prediction for helical transmembrane proteins at 86% accuracy B Rost , R Casadio , P Fariselli Protein Science , 1996 , 5 :1704-1718 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 PHD: predicting one-dimensional protein structure by profile based neural networks B Rost Methods in Enzymology , 1996 , 266 :525-539 Prediction of helical transmembrane segments at 95% accuracy B Rost , R Casadio , P Fariselli , C Sander Protein Science , 1995 , 4 :521-533 Methods:  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 Predicting protein subcellular localization using intelligent systems R Nair , B Rost Methods Mol Biol , 2008 , 484 :435-463 Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments D Przybylski , B Rost Nucleic Acids Research , 2007 , 35 :2238-2246 ISIS: Interaction Sites Identified from Sequence Y Ofran , B Rost Bioinformatics , 2007 , 23 :e13-16 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 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 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 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 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 DSSPcont: continuous secondary structure assignments for proteins P Carter , CAF Andersen , B Rost Nucleic Acids Research , 2003 , 31 :3293-3295 Non-coding RNA:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material 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 The transcriptional landscape of the mammalian genome P Carninci , et al. Science , 2005 , 309 :1559-1563 Prediction services:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material Predicting protein subcellular localization using intelligent systems R Nair , B Rost Methods Mol Biol , 2008 , 484 :435-463 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 : 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 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 PROFcon: novel prediction of long-range contacts M Punta , B Rost Bioinformatics , 2005 , 21 :2960-2968 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 UniqueProt: creating representative protein sequence sets S Mika , B Rost Nucleic Acids Research , 2003 , 31 :3789-3791 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 Protein binding:  abstr=Abstract, www=paper in HTML, pdf=paper in PDF, som=Supporting online material ISIS: Interaction Sites Identified from Sequence Y Ofran , B Rost Bioinformatics , 2007 , 23 :e13-16 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 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 The PredictProtein server B Rost , J Liu Nucleic Acids Research , 2003 , 31 :3300-3304 Finding nuclear localisation signals M Cokol , R Nair , B Rost EMBO Reports , 2000 , 1 :411-415 Protein function:  abstr=Abstract, www