Publications

Found 287 results
2008
Trott O, Siggers K, Rost B, Palmer AG. Protein conformational flexibility prediction using machine learning. J Magn Reson. 2008 ;192(1):37-47.
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.
Aramini JM, Rossi P, Huang YJ, Zhao L, Jiang M, Maglaqui M, Xiao R, Locke J, Nair R, Rost B, et al. Solution NMR structure of the NlpC/P60 domain of lipoprotein Spr from Escherichia coli: structural evidence for a novel cysteine peptidase catalytic triad. Biochemistry. 2008 ;47(37):9715-7.
Aramini JM, Sharma S, Huang YJ, Swapna GVT, Ho CKent, Shetty K, Cunningham K, Ma L-C, Zhao L, Owens LA, et al. Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis. Proteins. 2008 ;72(1):526-30.
2007
Przybylski D, Rost B. Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. Nucleic Acids Res. 2007 ;35(7):2238-46.
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.
Ofran Y, Rost B. ISIS: interaction sites identified from sequence. Bioinformatics. 2007 ;23(2):e13-6.
Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B. Membrane protein prediction methods. Methods. 2007 ;41(4):460-74.
Schlessinger A, Liu J, Rost B. Natively unstructured loops differ from other loops. PLoS Comput Biol. 2007 ;3(7):e140.
Schlessinger A, Punta M, Rost B. Natively unstructured regions in proteins identified from contact predictions. Bioinformatics. 2007 ;23(18):2376-84.
Liu J, Montelione GT, Rost B. Novel leverage of structural genomics. Nat Biotechnol. 2007 ;25(8):849-51.
Ofran Y, Mysore V, Rost B. Prediction of DNA-binding residues from sequence. Bioinformatics. 2007 ;23(13):i347-53.
Ofran Y, Rost B. Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol. 2007 ;3(7):e119.
Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 2007 ;35(11):3823-35.
Aramini JM, Huang YJ, Swapna GVT, Cort JR, Rajan PK, Xiao R, Shastry R, Acton TB, Liu J, Rost B, et al. Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family. Proteins. 2007 ;68(3):789-95.
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.
Liu J, Gough J, Rost B. Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet. 2006 ;2(4):e29.
Schlessinger A, Ofran Y, Yachdav G, Rost B. Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res. 2006 ;34(Database issue):D777-80.
Passerini A, Punta M, Ceroni A, Rost B, Frasconi P. Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins. 2006 ;65(2):305-16.
Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, et al. Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 2006 ;14(8):1211-7.
Schlessinger A, Yachdav G, Rost B. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 2006 ;22(7):891-3.
Bigelow H, Rost B. PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res. 2006 ;34(Web Server issue):W186-8.
Mika S, Rost B. Protein-protein interactions more conserved within species than across species. PLoS Comput Biol. 2006 ;2(7):e79.
2005
Benach J, Edstrom WC, Lee I, Das K, Cooper B, Xiao R, Liu J, Rost B, Acton TB, Montelione GT, et al. The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism. Acta Crystallogr D Biol Crystallogr. 2005 ;61(Pt 5):589-98.
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.
Snyder DA, Chen Y, Denissova NG, Acton T, Aramini JM, Ciano M, Karlin R, Liu J, Manor P, Rajan PA, et al. Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. J Am Chem Soc. 2005 ;127(47):16505-11.
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.
Graña O, Eyrich VA, Pazos F, Rost B, Valencia A. EVAcon: a protein contact prediction evaluation service. Nucleic Acids Res. 2005 ;33(Web Server issue):W347-51.
Nair R, Rost B. Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol. 2005 ;348(1):85-100.
Mika S, Rost B. NMPdb: Database of Nuclear Matrix Proteins. Nucleic Acids Res. 2005 ;33(Database issue):D160-3.
Punta M, Rost B. PROFcon: novel prediction of long-range contacts. Bioinformatics. 2005 ;21(13):2960-8.
Schlessinger A, Rost B. Protein flexibility and rigidity predicted from sequence. Proteins. 2005 ;61(1):115-26.
Punta M, Rost B. Protein folding rates estimated from contact predictions. J Mol Biol. 2005 ;348(3):507-12.
Powers R, Mirkovic N, Goldsmith-Fischman S, Acton TB, Chiang Y, Huang YJ, Ma L, Rajan PK, Cort JR, Kennedy MA, et al. Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes. Protein Sci. 2005 ;14(11):2849-61.
2004
Powers R, Acton TB, Chiang Y, Rajan PK, Cort JR, Kennedy MA, Liu J, Ma L, Rost B, Montelione GT. (1)H, (13)C and (15)N assignments for the Archaeglobus fulgidis protein AF2095. J Biomol NMR. 2004 ;30(1):107-8.
Liu J, Hegyi H, Acton TB, Montelione GT, Rost B. Automatic target selection for structural genomics on eukaryotes. Proteins. 2004 ;56(2):188-200.
Wrzeszczynski KO, Rost B. Cataloging proteins in cell cycle control. Methods Mol Biol. 2004 ;241:219-33.
Liu J, Rost B. CHOP: parsing proteins into structural domains. Nucleic Acids Res. 2004 ;32(Web Server issue):W569-71.
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.
Nair R, Rost B. LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. Nucleic Acids Res. 2004 ;32(Web Server issue):W517-21.
Mika S, Rost B. NLProt: extracting protein names and sequences from papers. Nucleic Acids Res. 2004 ;32(Web Server issue):W634-7.
Bigelow HR, Petrey DS, Liu J, Przybylski D, Rost B. Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res. 2004 ;32(8):2566-77.
Rost B, Yachdav G, Liu J. The PredictProtein server. Nucleic Acids Res. 2004 ;32(Web Server issue):W321-6.
Mika S, Rost B. Protein names precisely peeled off free text. Bioinformatics. 2004 ;20 Suppl 1:i241-7.
Wunderlich Z, Acton TB, Liu J, Kornhaber G, Everett J, Carter P, Lan N, Echols N, Gerstein M, Rost B, et al. The protein target list of the Northeast Structural Genomics Consortium. Proteins. 2004 ;56(2):181-7.
Liu J, Rost B. Sequence-based prediction of protein domains. Nucleic Acids Res. 2004 ;32(12):3522-30.
2003
Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol. 2003 ;325(2):377-87.

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