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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.
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.