Publications

Found 52 results
Filters: Keyword is Databases, Protein  [Clear All Filters]
2022
Bernhofer M, Rost B. TMbed: transmembrane proteins predicted through language model embeddings. BMC Bioinformatics. 2022 ;23(1):326.
2015
O'Donoghue SI, Sabir KS, Kalemanov M, Stolte C, Wellmann B, Ho V, Roos M, Perdigão N, Buske FA, Heinrich J, et al. Aquaria: simplifying discovery and insight from protein structures. Nat Methods. 2015 ;12(2):98-9.
2013
Radivojac P, Clark WT, Oron TRonnen, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, et al. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013 ;10(3):221-7.
2011
Rastogi S, Rost B. LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. Nucleic Acids Res. 2011 ;39(Database issue):D230-4.
2010
Schaefer C, Schlessinger A, Rost B. Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be. Bioinformatics. 2010 ;26(5):625-31.
Singarapu KKumar, Mills JL, Xiao R, Acton T, Punta M, Fischer M, Honig B, Rost B, Montelione GT, Szyperski T. Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. Proteins. 2010 ;78(3):779-84.
2009
Wrzeszczynski KO, Rost B. Cell cycle kinases predicted from conserved biophysical properties. Proteins. 2009 ;74(3):655-68.
Bromberg Y, Rost B. Correlating protein function and stability through the analysis of single amino acid substitutions. BMC Bioinformatics. 2009 ;10 Suppl 8:S8.
Schlessinger A, Punta M, Yachdav G, Kaján L, Rost B. Improved disorder prediction by combination of orthogonal approaches. PLoS One. 2009 ;4(2):e4433.
Galea CA, High AA, Obenauer JC, Mishra A, Park C-G, Punta M, Schlessinger A, Ma J, Rost B, Slaughter CA, et al. Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. J Proteome Res. 2009 ;8(1):211-26.
Bromberg Y, Yachdav G, Ofran Y, Schneider R, Rost B. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'. Curr Opin Drug Discov Devel. 2009 ;12(3):408-19.
Bigelow H, Rost B. Online tools for predicting integral membrane proteins. Methods Mol Biol. 2009 ;528:3-23.
Nair R, Liu J, Soong T-T, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, et al. Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics. 2009 ;10(2):181-91.
Bertonati C, Punta M, Fischer M, Yachdav G, Forouhar F, Zhou W, Kuzin AP, Seetharaman J, Abashidze M, Ramelot TA, et al. Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins. 2009 ;75(3):760-73.
Kernytsky A, Rost B. Using genetic algorithms to select most predictive protein features. Proteins. 2009 ;75(1):75-88.
2008
Ofran Y, Schlessinger A, Rost B. Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes. J Immunol. 2008 ;181(9):6230-5.
Lippi M, Passerini A, Punta M, Rost B, Frasconi P. MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. Bioinformatics. 2008 ;24(18):2094-5.
Punta M, Rost B. Neural networks predict protein structure and function. Methods Mol Biol. 2008 ;458:203-30.
Nair R, Rost B. Protein subcellular localization prediction using artificial intelligence technology. Methods Mol Biol. 2008 ;484:435-63.
Bromberg Y, Yachdav G, Rost B. SNAP predicts effect of mutations on protein function. Bioinformatics. 2008 ;24(20):2397-8.
2007
Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tramontano A. Critical assessment of methods of protein structure prediction-Round VII. Proteins. 2007 ;69 Suppl 8:3-9.
Schlessinger A, Liu J, Rost B. Natively unstructured loops differ from other loops. PLoS Comput Biol. 2007 ;3(7):e140.
Liu J, Montelione GT, Rost B. Novel leverage of structural genomics. Nat Biotechnol. 2007 ;25(8):849-51.
Ofran Y, Rost B. Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol. 2007 ;3(7):e119.
2006
Ofran Y, Yachdav G, Mozes E, Soong T-T, Nair R, Rost B. Create and assess protein networks through molecular characteristics of individual proteins. Bioinformatics. 2006 ;22(14):e402-7.
Schlessinger A, Ofran Y, Yachdav G, Rost B. Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res. 2006 ;34(Database issue):D777-80.
Schlessinger A, Yachdav G, Rost B. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 2006 ;22(7):891-3.
2005
Ofran Y, Punta M, Schneider R, Rost B. Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discov Today. 2005 ;10(21):1475-82.
Graña O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins. 2005 ;61 Suppl 7:214-24.
Moult J, Fidelis K, Rost B, Hubbard T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP)--round 6. Proteins. 2005 ;61 Suppl 7:3-7.
Mika S, Rost B. NMPdb: Database of Nuclear Matrix Proteins. Nucleic Acids Res. 2005 ;33(Database issue):D160-3.
Schlessinger A, Rost B. Protein flexibility and rigidity predicted from sequence. Proteins. 2005 ;61(1):115-26.
2004
Liu J, Hegyi H, Acton TB, Montelione GT, Rost B. Automatic target selection for structural genomics on eukaryotes. Proteins. 2004 ;56(2):188-200.
Liu J, Rost B. CHOP proteins into structural domain-like fragments. Proteins. 2004 ;55(3):678-88.
Przybylski D, Rost B. Improving fold recognition without folds. J Mol Biol. 2004 ;341(1):255-69.
Mika S, Rost B. NLProt: extracting protein names and sequences from papers. Nucleic Acids Res. 2004 ;32(Web Server issue):W634-7.
2003
Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol. 2003 ;325(2):377-87.
Nair R, Rost B. Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins. 2003 ;53(4):917-30.
Liu J, Rost B. Domains, motifs and clusters in the protein universe. Curr Opin Chem Biol. 2003 ;7(1):5-11.
Y Y Koh I, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, et al. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003 ;31(13):3311-5.
Nair R, Rost B. LOC3D: annotate sub-cellular localization for protein structures. Nucleic Acids Res. 2003 ;31(13):3337-40.
Nair R, Carter P, Rost B. NLSdb: database of nuclear localization signals. Nucleic Acids Res. 2003 ;31(1):397-9.
Carter P, Liu J, Rost B. PEP: Predictions for Entire Proteomes. Nucleic Acids Res. 2003 ;31(1):410-3.
Rost B, Liu J. The PredictProtein server. Nucleic Acids Res. 2003 ;31(13):3300-4.
Andersen CAF, Rost B. Secondary structure assignment. Methods Biochem Anal. 2003 ;44:341-63.
2002
Przybylski D, Rost B. Alignments grow, secondary structure prediction improves. Proteins. 2002 ;46(2):197-205.
Rost B. Enzyme function less conserved than anticipated. J Mol Biol. 2002 ;318(2):595-608.
Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins. 2002 ;47(2):228-35.
Nair R, Rost B. Inferring sub-cellular localization through automated lexical analysis. Bioinformatics. 2002 ;18 Suppl 1:S78-86.
Liu J, Tan H, Rost B. Loopy proteins appear conserved in evolution. J Mol Biol. 2002 ;322(1):53-64.

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