Publications

Found 274 results
2010
Rastogi S, Rost B. Bioinformatics predictions of localization and targeting. Methods Mol Biol. 2010 ;619:285-305.
Chen Y-H, Hu L, Punta M, Bruni R, Hillerich B, Kloss B, Rost B, Love J, Siegelbaum SA, Hendrickson WA. Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Nature. 2010 ;467(7319):1074-80.
Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N. MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Res. 2010 ;38(Web Server issue):W523-8.
Love J, Mancia F, Shapiro L, Punta M, Rost B, Girvin M, Wang D-N, Zhou M, Hunt JF, Szyperski T, et al. The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. J Struct Funct Genomics. 2010 ;11(3):191-9.
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.
Tang Y, Xiao R, Ciccosanti C, Janjua H, Lee DYup, Everett JK, Swapna GVT, Acton TB, Rost B, Montelione GT. Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG. Proteins. 2010 ;78(11):2563-8.
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.
Aramini JM, Tubbs JL, Kanugula S, Rossi P, Ertekin A, Maglaqui M, Hamilton K, Ciccosanti CT, Jiang M, Xiao R, et al. Structural basis of O6-alkylguanine recognition by a bacterial alkyltransferase-like DNA repair protein. J Biol Chem. 2010 ;285(18):13736-41.
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.
Moult J, Fidelis K, Kryshtafovych A, Rost B, Tramontano A. Critical assessment of methods of protein structure prediction - Round VIII. Proteins. 2009 ;77 Suppl 9:1-4.
Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, Tramontano A. Evaluation of template-based models in CASP8 with standard measures. Proteins. 2009 ;77 Suppl 9:18-28.
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.

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