Publications

Found 37 results
Filters: Keyword is Amino Acid Sequence  [Clear All Filters]
2015
O'Donoghue SI, Sabir KS, Kalemanov M, Stolte C, Wellmann B, Ho V, Roos M, Perdigão N, Buske FA, Heinrich J, et al. Aquaria: simplifying discovery and insight from protein structures. Nat Methods. 2015 ;12(2):98-9.
Guo Y, Kalathur RC, Liu Q, Kloss B, Bruni R, Ginter C, Kloppmann E, Rost B, Hendrickson WA. Protein structure. Structure and activity of tryptophan-rich TSPO proteins. Science. 2015 ;347(6221):551-5.
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.
2012
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.
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
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.
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.
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.
2009
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.
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.
2008
Bromberg Y, Rost B. Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics. 2008 ;24(16):i207-12.
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.
Przybylski D, Rost B. Powerful fusion: PSI-BLAST and consensus sequences. Bioinformatics. 2008 ;24(18):1987-93.
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.
Schlessinger A, Liu J, Rost B. Natively unstructured loops differ from other loops. PLoS Comput Biol. 2007 ;3(7):e140.
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.
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
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.
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.
Mika S, Rost B. NMPdb: Database of Nuclear Matrix Proteins. Nucleic Acids Res. 2005 ;33(Database issue):D160-3.
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.
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.
Mika S, Rost B. NLProt: extracting protein names and sequences from papers. Nucleic Acids Res. 2004 ;32(Web Server issue):W634-7.
2003
Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol. 2003 ;325(2):377-87.
Carter P, Andersen CAF, Rost B. DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res. 2003 ;31(13):3293-5.
Rost B. Prediction in 1D: secondary structure, membrane helices, and accessibility. Methods Biochem Anal. 2003 ;44:559-87.
Andersen CAF, Rost B. Secondary structure assignment. Methods Biochem Anal. 2003 ;44:341-63.
Aramini JM, Huang YJ, Cort JR, Goldsmith-Fischman S, Xiao R, Shih L-Y, Ho CK, Liu J, Rost B, Honig B, et al. Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci. 2003 ;12(12):2823-30.
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. Enzyme function less conserved than anticipated. J Mol Biol. 2002 ;318(2):595-608.
Nair R, Rost B. Sequence conserved for subcellular localization. Protein Sci. 2002 ;11(12):2836-47.