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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.
2014
Cejuela JMiguel
,
McQuilton P
,
Ponting L
,
Marygold SJ
,
Stefancsik R
,
Millburn GH
,
Rost B
.
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Database (Oxford). 2014 ;2014:bau033.
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.
2012
Goldberg T
,
Hamp T
,
Rost B
.
LocTree2 predicts localization for all domains of life.
Bioinformatics. 2012 ;28(18):i458-i465.
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.
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.
2010
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.
2009
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.
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.
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.
Nair R
,
Rost B
.
Protein subcellular localization prediction using artificial intelligence technology.
Methods Mol Biol. 2008 ;484:435-63.
2007
Schlessinger A
,
Liu J
,
Rost B
.
Natively unstructured loops differ from other loops.
PLoS Comput Biol. 2007 ;3(7):e140.
2006
Liu J
,
Gough J
,
Rost B
.
Distinguishing protein-coding from non-coding RNAs through support vector machines.
PLoS Genet. 2006 ;2(4):e29.
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.
Punta M
,
Rost B
.
Protein folding rates estimated from contact predictions.
J Mol Biol. 2005 ;348(3):507-12.
2004
Wrzeszczynski KO
,
Rost B
.
Cataloging proteins in cell cycle control.
Methods Mol Biol. 2004 ;241:219-33.
2003
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.
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
.
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.
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.
Chen CPeter
,
Kernytsky A
,
Rost B
.
Transmembrane helix predictions revisited.
Protein Sci. 2002 ;11(12):2774-91.