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Protein Conformation
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2021
Bernhofer M
,
Dallago C
,
Karl T
,
Satagopam V
,
Heinzinger M
,
Littmann M
,
Olenyi T
,
Qiu J
,
Schütze K
,
Yachdav G
, et al.
PredictProtein - Predicting Protein Structure and Function for 29 Years.
Nucleic Acids Res. 2021 ;49(W1):W535-W540.
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.
2015
O'Donoghue SI
,
Sabir KS
,
Kalemanov M
,
Stolte C
,
Wellmann B
,
Ho V
,
Roos M
,
Perdigão N
,
Buske FA
,
Heinrich J
, et al.
Aquaria: simplifying discovery and insight from protein structures.
Nat Methods. 2015 ;12(2):98-9.
Guo Y
,
Kalathur RC
,
Liu Q
,
Kloss B
,
Bruni R
,
Ginter C
,
Kloppmann E
,
Rost B
,
Hendrickson WA
.
Protein structure. Structure and activity of tryptophan-rich TSPO proteins.
Science. 2015 ;347(6221):551-5.
2014
Kaján L
,
Hopf TA
,
Kalaš M
,
Marks DS
,
Rost B
.
FreeContact: fast and free software for protein contact prediction from residue co-evolution.
BMC Bioinformatics. 2014 ;15:85.
Yachdav G
,
Kloppmann E
,
Kaján L
,
Hecht M
,
Goldberg T
,
Hamp T
,
Hönigschmid P
,
Schafferhans A
,
Roos M
,
Bernhofer M
, et al.
PredictProtein--an open resource for online prediction of protein structural and functional features.
Nucleic Acids Res. 2014 ;42(Web Server issue):W337-43.
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.
2012
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
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.
2010
Wainreb G
,
Ashkenazy H
,
Bromberg Y
,
Starovolsky-Shitrit A
,
Haliloglu T
,
Ruppin E
,
Avraham KB
,
Rost B
,
Ben-Tal N
.
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.
Nucleic Acids Res. 2010 ;38(Web Server issue):W523-8.
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.
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.
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.
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.
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.
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.
Kernytsky A
,
Rost B
.
Using genetic algorithms to select most predictive protein features.
Proteins. 2009 ;75(1):75-88.
2008
Punta M
,
Rost B
.
Neural networks predict protein structure and function.
Methods Mol Biol. 2008 ;458:203-30.
Trott O
,
Siggers K
,
Rost B
,
Palmer AG
.
Protein conformational flexibility prediction using machine learning.
J Magn Reson. 2008 ;192(1):37-47.
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.
Punta M
,
Forrest LR
,
Bigelow H
,
Kernytsky A
,
Liu J
,
Rost B
.
Membrane protein prediction methods.
Methods. 2007 ;41(4):460-74.
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
Schlessinger A
,
Yachdav G
,
Rost B
.
PROFbval: predict flexible and rigid residues in proteins.
Bioinformatics. 2006 ;22(7):891-3.
2005
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.
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.
Rost B
,
Yachdav G
,
Liu J
.
The PredictProtein server.
Nucleic Acids Res. 2004 ;32(Web Server issue):W321-6.
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.
2003
Ofran Y
,
Rost B
.
Analysing six types of protein-protein interfaces.
J Mol Biol. 2003 ;325(2):377-87.
Y Y Koh I
,
Eyrich VA
,
Marti-Renom MA
,
Przybylski D
,
Madhusudhan MS
,
Eswar N
,
Graña O
,
Pazos F
,
Valencia A
,
Sali A
, et al.
EVA: Evaluation of protein structure prediction servers.
Nucleic Acids Res. 2003 ;31(13):3311-5.
Nair R
,
Rost B
.
LOC3D: annotate sub-cellular localization for protein structures.
Nucleic Acids Res. 2003 ;31(13):3337-40.
Eyrich VA
,
Rost B
.
META-PP: single interface to crucial prediction servers.
Nucleic Acids Res. 2003 ;31(13):3308-10.
Carter P
,
Liu J
,
Rost B
.
PEP: Predictions for Entire Proteomes.
Nucleic Acids Res. 2003 ;31(1):410-3.
Ofran Y
,
Rost B
.
Predicted protein-protein interaction sites from local sequence information.
FEBS Lett. 2003 ;544(1-3):236-9.
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
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.