Publications

Found 259 results
2009
Schlessinger A, Punta M, Yachdav G, Kaján L, Rost B. Improved disorder prediction by combination of orthogonal approaches. PLoS One. 2009 ;4(2):e4433.
Bromberg Y, Overton J, Vaisse C, Leibel RL, Rost B. In silico mutagenesis: a case study of the melanocortin 4 receptor. FASEB J. 2009 ;23(9):3059-69.
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.
Liu G, Forouhar F, Eletsky A, Atreya HS, Aramini JM, Xiao R, Huang YJ, Abashidze M, Seetharaman J, Liu J, et al. NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway. J Struct Funct Genomics. 2009 ;10(2):127-36.
Eletsky A, Sukumaran DK, Xiao R, Acton TB, Rost B, Montelione GT, Szyperski T. NMR structure of protein YvyC from Bacillus subtilis reveals unexpected structural similarity between two PFAM families. Proteins. 2009 ;76(4):1037-41.
Bigelow H, Rost B. Online tools for predicting integral membrane proteins. Methods Mol Biol. 2009 ;528:3-23.
Dessailly BH, Nair R, Jaroszewski L, J Fajardo E, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C. PSI-2: structural genomics to cover protein domain family space. Structure. 2009 ;17(6):869-81.
Rossi P, Aramini JM, Xiao R, Chen CX, Nwosu C, Owens LA, Maglaqui M, Nair R, Fischer M, Acton TB, et al. Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus. Proteins. 2009 ;74(2):515-9.
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.
Punta M, Love J, Handelman S, Hunt JF, Shapiro L, Hendrickson WA, Rost B. Structural genomics target selection for the New York consortium on membrane protein structure. J Struct Funct Genomics. 2009 ;10(4):255-68.
W Price N, Chen Y, Handelman SK, Neely H, Manor P, Karlin R, Nair R, Liu J, Baran M, Everett J, et al. Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nat Biotechnol. 2009 ;27(1):51-7.
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.
Bromberg Y, Rost B. Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics. 2008 ;24(16):i207-12.
Linial M, Mesirov JP, McKay BJMorrison, Rost B. ISMB 2008 Toronto. PLoS Comput Biol. 2008 ;4(6):e1000094.
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.
Singarapu KKumar, Xiao R, Acton T, Rost B, Montelione GT, Szyperski T. 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. Proteins. 2008 ;71(2):1027-31.
Soong T-T, Wrzeszczynski KO, Rost B. Physical protein-protein interactions predicted from microarrays. Bioinformatics. 2008 ;24(22):2608-14.
Przybylski D, Rost B. Powerful fusion: PSI-BLAST and consensus sequences. Bioinformatics. 2008 ;24(18):1987-93.
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.

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