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Found 38 results
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Sequence Analysis, Protein
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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.
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.
2012
Goldberg T
,
Hamp T
,
Rost B
.
LocTree2 predicts localization for all domains of life.
Bioinformatics. 2012 ;28(18):i458-i465.
2009
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.
Bigelow H
,
Rost B
.
Online tools for predicting integral membrane proteins.
Methods Mol Biol. 2009 ;528:3-23.
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.
2008
Bromberg Y
,
Rost B
.
Comprehensive in silico mutagenesis highlights functionally important residues in proteins.
Bioinformatics. 2008 ;24(16):i207-12.
Lippi M
,
Passerini A
,
Punta M
,
Rost B
,
Frasconi P
.
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
Bioinformatics. 2008 ;24(18):2094-5.
Przybylski D
,
Rost B
.
Powerful fusion: PSI-BLAST and consensus sequences.
Bioinformatics. 2008 ;24(18):1987-93.
2007
Przybylski D
,
Rost B
.
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments.
Nucleic Acids Res. 2007 ;35(7):2238-46.
Ofran Y
,
Rost B
.
ISIS: interaction sites identified from sequence.
Bioinformatics. 2007 ;23(2):e13-6.
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.
Bromberg Y
,
Rost B
.
SNAP: predict effect of non-synonymous polymorphisms on function.
Nucleic Acids Res. 2007 ;35(11):3823-35.
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.
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.
2005
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.
Punta M
,
Rost B
.
PROFcon: novel prediction of long-range contacts.
Bioinformatics. 2005 ;21(13):2960-8.
2004
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.
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.
Liu J
,
Rost B
.
Sequence-based prediction of protein domains.
Nucleic Acids Res. 2004 ;32(12):3522-30.
2003
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.
Liu J
,
Rost B
.
NORSp: Predictions of long regions without regular secondary structure.
Nucleic Acids Res. 2003 ;31(13):3833-5.
Rost B
,
Liu J
.
The PredictProtein server.
Nucleic Acids Res. 2003 ;31(13):3300-4.
Kernytsky A
,
Rost B
.
Static benchmarking of membrane helix predictions.
Nucleic Acids Res. 2003 ;31(13):3642-4.
Mika S
,
Rost B
.
UniqueProt: Creating representative protein sequence sets.
Nucleic Acids Res. 2003 ;31(13):3789-91.
2002
Nair R
,
Rost B
.
Inferring sub-cellular localization through automated lexical analysis.
Bioinformatics. 2002 ;18 Suppl 1:S78-86.
Liu J
,
Rost B
.
Target space for structural genomics revisited.
Bioinformatics. 2002 ;18(7):922-33.