Found 254 results
Hamp T, Goldberg T, Rost B. Accelerating the Original Profile Kernel. PLoS One. 2013 ;8(6):e68459.
Kaján L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angermüller C, Böhm A, Domke S, Ertl J, Mertes C, et al. Cloud prediction of protein structure and function with PredictProtein for Debian. Biomed Res Int. 2013 ;2013:398968.
Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, et al. Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nat Struct Mol Biol. 2013 ;20(2):135-8.
Mistry J, Kloppmann E, Rost B, Punta M. An estimated 5% of new protein structures solved today represent a new Pfam family. Acta Crystallogr D Biol Crystallogr. 2013 ;69(Pt 11):2186-93.
Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, et al. Homology-based inference sets the bar high for protein function prediction. BMC Bioinformatics. 2013 ;14 Suppl 3:S7.
Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B. ISCB computational biology Wikipedia competition. PLoS Comput Biol. 2013 ;9(9):e1003242.
Rost B. ISCB: past-present perspective for the International Society for Computational Biology. Bioinformatics. 2013 ;29(24):3243-5.
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.
Bromberg Y, Kahn PC, Rost B. Neutral and weakly nonneutral sequence variants may define individuality. Proc Natl Acad Sci U S A. 2013 ;110(35):14255-60.
Hecht M, Bromberg Y, Rost B. News from the protein mutability landscape. J Mol Biol. 2013 ;425(21):3937-48.
Hamp T, Rost B. Alternative protein-protein interfaces are frequent exceptions. PLoS Comput Biol. 2012 ;8(8):e1002623.
Schaefer C, Bromberg Y, Achten D, Rost B. Disease-related mutations predicted to impact protein function. BMC Genomics. 2012 ;13 Suppl 4:S11.
Goldberg T, Hamp T, Rost B. LocTree2 predicts localization for all domains of life. Bioinformatics. 2012 ;28(18):i458-i465.
Wu Y, Punta M, Xiao R, Acton TB, Sathyamoorthy B, Dey F, Fischer M, Skerra A, Rost B, Montelione GT, et al. NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PLoS One. 2012 ;7(6):e37404.
Rost B, Gaasterland T, Lengauer T, Linial M, Markel S, McKay BJMorrison, Schneider R, Horton P, Kelso J. Paving the future: finding suitable ISMB venues. Bioinformatics. 2012 ;28(19):2556-9.
Schaefer C, Rost B. Predict impact of single amino acid change upon protein structure. BMC Genomics. 2012 ;13 Suppl 4:S4.
Schaefer C, Meier A, Rost B, Bromberg Y. SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics. 2012 ;28(4):601-2.
Snyder DA, Aramini JM, Yu B, Huang YJ, Xiao R, Cort JR, Shastry R, Ma L-C, Liu J, Rost B, et al. Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. Proteins. 2012 ;80(7):1901-6.
Kloppmann E, Punta M, Rost B. Structural genomics plucks high-hanging membrane proteins. Curr Opin Struct Biol. 2012 ;22(3):326-32.
Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS. Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 2012 ;149(7):1607-21.
Shi W, Punta M, Bohon J, J Sauder M, D'Mello R, Sullivan M, Toomey J, Abel D, Lippi M, Passerini A, et al. Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy. Genome Res. 2011 ;21(6):898-907.
Offman MN, Krol M, Rost B, Silman I, Sussman JL, Futerman AH. Comparison of a molecular dynamics model with the X-ray structure of the N370S acid-beta-glucosidase mutant that causes Gaucher disease. Protein Eng Des Sel. 2011 ;24(10):773-5.
Cao Y, Jin X, Levin EJ, Huang H, Zong Y, Quick M, Weng J, Pan Y, Love J, Punta M, et al. Crystal structure of a phosphorylation-coupled saccharide transporter. Nature. 2011 ;473(7345):50-4.
Cao Y, Jin X, Huang H, Derebe MGetahun, Levin EJ, Kabaleeswaran V, Pan Y, Punta M, Love J, Weng J, et al. Crystal structure of a potassium ion transporter, TrkH. Nature. 2011 ;471(7338):336-40.
Schönbach C, Tan TWee, Kelso J, Rost B, Nathan S, Ranganathan S. InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia. BMC Genomics. 2011 ;12 Suppl 3:S1.
Lathrop RH, Rost B. ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature. PLoS Comput Biol. 2011 ;7(2):e1002014.
Lathrop RH, Rost B. ISCB public policy statement on open access to scientific and technical research literature. Bioinformatics. 2011 ;27(3):291-4.
W Price N, Handelman SK, Everett JK, Tong SN, Bracic A, Luff JD, Naumov V, Acton T, Manor P, Xiao R, et al. Large-scale experimental studies show unexpected amino acid effects on protein expression and solubility in vivo in E. coli. Microb Inform Exp. 2011 ;1(1):6.
Rastogi S, Rost B. LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. Nucleic Acids Res. 2011 ;39(Database issue):D230-4.
Zimprich A, Benet-Pagès A, Struhal W, Graf E, Eck SH, Offman MN, Haubenberger D, Spielberger S, Schulte EC, Lichtner P, et al. A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease. Am J Hum Genet. 2011 ;89(1):168-75.
Schlessinger A, Schaefer C, Vicedo E, Schmidberger M, Punta M, Rost B. Protein disorder--a breakthrough invention of evolution?. Curr Opin Struct Biol. 2011 ;21(3):412-8.
Yang Y, Ramelot TA, Cort JR, Wang D, Ciccosanti C, Hamilton K, Nair R, Rost B, Acton TB, Xiao R, et al. Solution NMR structure of photosystem II reaction center protein Psb28 from Synechocystis sp. Strain PCC 6803. Proteins. 2011 ;79(1):340-4.
Ranganathan S, Schönbach C, Kelso J, Rost B, Nathan S, Tan TWee. Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. BMC Bioinformatics. 2011 ;12 Suppl 13:S1.
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.
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.