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Found 51 results
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Databases, Protein
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Author
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Rost, Burkhard
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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.
2013
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.
2011
Rastogi S
,
Rost B
.
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana.
Nucleic Acids Res. 2011 ;39(Database issue):D230-4.
2010
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.
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.
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.
Schlessinger A
,
Punta M
,
Yachdav G
,
Kaján L
,
Rost B
.
Improved disorder prediction by combination of orthogonal approaches.
PLoS One. 2009 ;4(2):e4433.
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.
Bigelow H
,
Rost B
.
Online tools for predicting integral membrane proteins.
Methods Mol Biol. 2009 ;528:3-23.
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.
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.
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.
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.
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.
Schlessinger A
,
Liu J
,
Rost B
.
Natively unstructured loops differ from other loops.
PLoS Comput Biol. 2007 ;3(7):e140.
Liu J
,
Montelione GT
,
Rost B
.
Novel leverage of structural genomics.
Nat Biotechnol. 2007 ;25(8):849-51.
Ofran Y
,
Rost B
.
Protein-protein interaction hotspots carved into sequences.
PLoS Comput Biol. 2007 ;3(7):e119.
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.
Schlessinger A
,
Ofran Y
,
Yachdav G
,
Rost B
.
Epitome: database of structure-inferred antigenic epitopes.
Nucleic Acids Res. 2006 ;34(Database issue):D777-80.
Schlessinger A
,
Yachdav G
,
Rost B
.
PROFbval: predict flexible and rigid residues in proteins.
Bioinformatics. 2006 ;22(7):891-3.
2005
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.
Moult J
,
Fidelis K
,
Rost B
,
Hubbard T
,
Tramontano A
.
Critical assessment of methods of protein structure prediction (CASP)--round 6.
Proteins. 2005 ;61 Suppl 7:3-7.
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.
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.
Liu J
,
Rost B
.
CHOP proteins into structural domain-like fragments.
Proteins. 2004 ;55(3):678-88.
Przybylski D
,
Rost B
.
Improving fold recognition without folds.
J Mol Biol. 2004 ;341(1):255-69.
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.
Nair R
,
Rost B
.
Better prediction of sub-cellular localization by combining evolutionary and structural information.
Proteins. 2003 ;53(4):917-30.
Liu J
,
Rost B
.
Domains, motifs and clusters in the protein universe.
Curr Opin Chem Biol. 2003 ;7(1):5-11.
Y Y Koh I
,
Eyrich VA
,
Marti-Renom MA
,
Przybylski D
,
Madhusudhan MS
,
Eswar N
,
Graña O
,
Pazos F
,
Valencia A
,
Sali A
, et al.
EVA: Evaluation of protein structure prediction servers.
Nucleic Acids Res. 2003 ;31(13):3311-5.
Nair R
,
Rost B
.
LOC3D: annotate sub-cellular localization for protein structures.
Nucleic Acids Res. 2003 ;31(13):3337-40.
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.
Rost B
,
Liu J
.
The PredictProtein server.
Nucleic Acids Res. 2003 ;31(13):3300-4.
Andersen CAF
,
Rost B
.
Secondary structure assignment.
Methods Biochem Anal. 2003 ;44:341-63.
2002
Przybylski D
,
Rost B
.
Alignments grow, secondary structure prediction improves.
Proteins. 2002 ;46(2):197-205.
Rost B
.
Enzyme function less conserved than anticipated.
J Mol Biol. 2002 ;318(2):595-608.
Pollastri G
,
Przybylski D
,
Rost B
,
Baldi P
.
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles.
Proteins. 2002 ;47(2):228-35.
Nair R
,
Rost B
.
Inferring sub-cellular localization through automated lexical analysis.
Bioinformatics. 2002 ;18 Suppl 1:S78-86.
Liu J
,
Tan H
,
Rost B
.
Loopy proteins appear conserved in evolution.
J Mol Biol. 2002 ;322(1):53-64.
Nair R
,
Rost B
.
Sequence conserved for subcellular localization.
Protein Sci. 2002 ;11(12):2836-47.
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