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Models, Molecular
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2021
O'Donoghue SI
,
Schafferhans A
,
Sikta N
,
Stolte C
,
Kaur S
,
Ho BK
,
Anderson S
,
Procter JB
,
Dallago C
,
Bordin N
, et al.
SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms.
Mol Syst Biol. 2021 ;17(9):e10079.
2020
Qiu J
,
Nechaev D
,
Rost B
.
Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human.
BMC Bioinformatics. 2020 ;21(1):452.
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.
2012
Snyder DA
,
Aramini JM
,
Yu B
,
Huang YJ
,
Xiao R
,
Cort JR
,
Shastry R
,
Ma L-C
,
Liu J
,
Rost B
, et al.
Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus.
Proteins. 2012 ;80(7):1901-6.
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
Cao Y
,
Jin X
,
Levin EJ
,
Huang H
,
Zong Y
,
Quick M
,
Weng J
,
Pan Y
,
Love J
,
Punta M
, et al.
Crystal structure of a phosphorylation-coupled saccharide transporter.
Nature. 2011 ;473(7345):50-4.
Cao Y
,
Jin X
,
Huang H
,
Derebe MGetahun
,
Levin EJ
,
Kabaleeswaran V
,
Pan Y
,
Punta M
,
Love J
,
Weng J
, et al.
Crystal structure of a potassium ion transporter, TrkH.
Nature. 2011 ;471(7338):336-40.
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.
Tang Y
,
Xiao R
,
Ciccosanti C
,
Janjua H
,
Lee DYup
,
Everett JK
,
Swapna GVT
,
Acton TB
,
Rost B
,
Montelione GT
.
Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG.
Proteins. 2010 ;78(11):2563-8.
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.
Moult J
,
Fidelis K
,
Kryshtafovych A
,
Rost B
,
Tramontano A
.
Critical assessment of methods of protein structure prediction - Round VIII.
Proteins. 2009 ;77 Suppl 9:1-4.
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.
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
,
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.
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
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.
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
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.
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.
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.
2006
Schlessinger A
,
Ofran Y
,
Yachdav G
,
Rost B
.
Epitome: database of structure-inferred antigenic epitopes.
Nucleic Acids Res. 2006 ;34(Database issue):D777-80.
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.
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.
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.
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.
Punta M
,
Rost B
.
PROFcon: novel prediction of long-range contacts.
Bioinformatics. 2005 ;21(13):2960-8.
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
Przybylski D
,
Rost B
.
Improving fold recognition without folds.
J Mol Biol. 2004 ;341(1):255-69.
2003
Carter P
,
Andersen CAF
,
Rost B
.
DSSPcont: Continuous secondary structure assignments for proteins.
Nucleic Acids Res. 2003 ;31(13):3293-5.
Eyrich VA
,
Rost B
.
META-PP: single interface to crucial prediction servers.
Nucleic Acids Res. 2003 ;31(13):3308-10.
Ofran Y
,
Rost B
.
Predicted protein-protein interaction sites from local sequence information.
FEBS Lett. 2003 ;544(1-3):236-9.
Rost B
.
Prediction in 1D: secondary structure, membrane helices, and accessibility.
Methods Biochem Anal. 2003 ;44:559-87.
Andersen CAF
,
Rost B
.
Secondary structure assignment.
Methods Biochem Anal. 2003 ;44:341-63.
Aramini JM
,
Huang YJ
,
Cort JR
,
Goldsmith-Fischman S
,
Xiao R
,
Shih L-Y
,
Ho CK
,
Liu J
,
Rost B
,
Honig B
, et al.
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii.
Protein Sci. 2003 ;12(12):2823-30.
2002
Andersen CAF
,
Palmer AG
,
Brunak S
,
Rost B
.
Continuum secondary structure captures protein flexibility.
Structure. 2002 ;10(2):175-84.
Chen CPeter
,
Rost B
.
Long membrane helices and short loops predicted less accurately.
Protein Sci. 2002 ;11(12):2766-73.
Liu J
,
Tan H
,
Rost B
.
Loopy proteins appear conserved in evolution.
J Mol Biol. 2002 ;322(1):53-64.
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.
Chen CPeter
,
Rost B
.
State-of-the-art in membrane protein prediction.
Appl Bioinformatics. 2002 ;1(1):21-35.
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