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Publications
Found 259 results
2009
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.
2007
Przybylski D
,
Rost B
.
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments.
Nucleic Acids Res. 2007 ;35(7):2238-46.
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.
Ofran Y
,
Rost B
.
ISIS: interaction sites identified from sequence.
Bioinformatics. 2007 ;23(2):e13-6.
Punta M
,
Forrest LR
,
Bigelow H
,
Kernytsky A
,
Liu J
,
Rost B
.
Membrane protein prediction methods.
Methods. 2007 ;41(4):460-74.
Schlessinger A
,
Liu J
,
Rost B
.
Natively unstructured loops differ from other loops.
PLoS Comput Biol. 2007 ;3(7):e140.
Schlessinger A
,
Punta M
,
Rost B
.
Natively unstructured regions in proteins identified from contact predictions.
Bioinformatics. 2007 ;23(18):2376-84.
Liu J
,
Montelione GT
,
Rost B
.
Novel leverage of structural genomics.
Nat Biotechnol. 2007 ;25(8):849-51.
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.
Bromberg Y
,
Rost B
.
SNAP: predict effect of non-synonymous polymorphisms on function.
Nucleic Acids Res. 2007 ;35(11):3823-35.
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
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.
Liu J
,
Gough J
,
Rost B
.
Distinguishing protein-coding from non-coding RNAs through support vector machines.
PLoS Genet. 2006 ;2(4):e29.
Schlessinger A
,
Ofran Y
,
Yachdav G
,
Rost B
.
Epitome: database of structure-inferred antigenic epitopes.
Nucleic Acids Res. 2006 ;34(Database issue):D777-80.
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.
Berman HM
,
Burley SK
,
Chiu W
,
Sali A
,
Adzhubei A
,
Bourne PE
,
Bryant SH
,
Dunbrack RL
,
Fidelis K
,
Frank J
, et al.
Outcome of a workshop on archiving structural models of biological macromolecules.
Structure. 2006 ;14(8):1211-7.
Schlessinger A
,
Yachdav G
,
Rost B
.
PROFbval: predict flexible and rigid residues in proteins.
Bioinformatics. 2006 ;22(7):891-3.
Bigelow H
,
Rost B
.
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
Nucleic Acids Res. 2006 ;34(Web Server issue):W186-8.
Mika S
,
Rost B
.
Protein-protein interactions more conserved within species than across species.
PLoS Comput Biol. 2006 ;2(7):e79.
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.
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.
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.
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