Publications

Found 44 results
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2020
Qiu J, Bernhofer M, Heinzinger M, Kemper S, Norambuena T, Melo F, Rost B. ProNA2020 predicts protein-DNA, protein-RNA, and protein-protein binding proteins and residues from sequence. J Mol Biol. 2020 ;432(7):2428-2443.
Qiu J, Nechaev D, Rost B. Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human. BMC Bioinformatics. 2020 ;21(1):452.
Reeb J, Wirth T, Rost B. Variant effect predictions capture some aspects of deep mutational scanning experiments. BMC Bioinformatics. 2020 ;21(1):107.
2014
Feiglin A, Ashkenazi S, Schlessinger A, Rost B, Ofran Y. Co-expression and co-localization of hub proteins and their partners are encoded in protein sequence. Mol Biosyst. 2014 ;10(4):787-94.
Chang Y, Bruni R, Kloss B, Assur Z, Kloppmann E, Rost B, Hendrickson WA, Liu Q. Structural basis for a pH-sensitive calcium leak across membranes. Science. 2014 ;344(6188):1131-5.
Yang T, Liu Q, Kloss B, Bruni R, Kalathur RC, Guo Y, Kloppmann E, Rost B, Colecraft HM, Hendrickson WA. Structure and selectivity in bestrophin ion channels. Science. 2014 ;346(6207):355-9.
2013
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.
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.
2012
Schaefer C, Bromberg Y, Achten D, Rost B. Disease-related mutations predicted to impact protein function. BMC Genomics. 2012 ;13 Suppl 4:S11.
Schaefer C, Meier A, Rost B, Bromberg Y. SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics. 2012 ;28(4):601-2.
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.
2011
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.
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.
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.
2010
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.
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.
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.
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.
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.
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.
2008
Punta M, Rost B. Neural networks predict protein structure and function. Methods Mol Biol. 2008 ;458:203-30.
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.
Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 2007 ;35(11):3823-35.
2006
Mika S, Rost B. Protein-protein interactions more conserved within species than across species. PLoS Comput Biol. 2006 ;2(7):e79.
2005
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.
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.
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
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.
2003
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.
Zidovetzki R, Rost B, Armstrong DL, Pecht I. Transmembrane domains in the functions of Fc receptors. Biophys Chem. 2003 ;100(1-3):555-75.
2002
Rost B, Honig B, Valencia A. Bioinformatics in structural genomics. Bioinformatics. 2002 ;18(7):897-8.
Rost B. Did evolution leap to create the protein universe?. Curr Opin Struct Biol. 2002 ;12(3):409-16.
Rost B. Enzyme function less conserved than anticipated. J Mol Biol. 2002 ;318(2):595-608.
Nair R, Rost B. Inferring sub-cellular localization through automated lexical analysis. Bioinformatics. 2002 ;18 Suppl 1:S78-86.
Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure. 2002 ;10(3):435-40.
Liu J, Rost B. Target space for structural genomics revisited. Bioinformatics. 2002 ;18(7):922-33.