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Publications
Found 287 results
2008
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.
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.
Graña O
,
Eyrich VA
,
Pazos F
,
Rost B
,
Valencia A
.
EVAcon: a protein contact prediction evaluation service.
Nucleic Acids Res. 2005 ;33(Web Server issue):W347-51.
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.
Punta M
,
Rost B
.
PROFcon: novel prediction of long-range contacts.
Bioinformatics. 2005 ;21(13):2960-8.
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.
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
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.
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.
Liu J
,
Rost B
.
CHOP: parsing proteins into structural domains.
Nucleic Acids Res. 2004 ;32(Web Server issue):W569-71.
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.
Nair R
,
Rost B
.
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets.
Nucleic Acids Res. 2004 ;32(Web Server issue):W517-21.
Mika S
,
Rost B
.
NLProt: extracting protein names and sequences from papers.
Nucleic Acids Res. 2004 ;32(Web Server issue):W634-7.
Bigelow HR
,
Petrey DS
,
Liu J
,
Przybylski D
,
Rost B
.
Predicting transmembrane beta-barrels in proteomes.
Nucleic Acids Res. 2004 ;32(8):2566-77.
Rost B
,
Yachdav G
,
Liu J
.
The PredictProtein server.
Nucleic Acids Res. 2004 ;32(Web Server issue):W321-6.
Mika S
,
Rost B
.
Protein names precisely peeled off free text.
Bioinformatics. 2004 ;20 Suppl 1:i241-7.
Wunderlich Z
,
Acton TB
,
Liu J
,
Kornhaber G
,
Everett J
,
Carter P
,
Lan N
,
Echols N
,
Gerstein M
,
Rost B
, et al.
The protein target list of the Northeast Structural Genomics Consortium.
Proteins. 2004 ;56(2):181-7.
Liu J
,
Rost B
.
Sequence-based prediction of protein domains.
Nucleic Acids Res. 2004 ;32(12):3522-30.
2003
Ofran Y
,
Rost B
.
Analysing six types of protein-protein interfaces.
J Mol Biol. 2003 ;325(2):377-87.
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