Home LiteratureArticle Details

PMID: 18812365 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

DOCKGROUND protein-protein docking decoy set.

Bioinformatics (Oxford, England) ·Vol. 24 ·No. 22 ·2008-11-15 ·Pages 2634-5

Liu S, Gao Y, Vakser IA

Abstract

A protein-protein docking decoy set is built for the Dockground unbound benchmark set. The GRAMM-X docking scan was used to generate 100 non-native and at least one near-native match per complex for 61 complexes. The set is a publicly available resource for the development of scoring functions and knowledge-based potentials for protein docking methodologies. The decoys are freely available for download at http://dockground.bioinformatics.ku.edu/UNBOUND/decoy/decoy.php

MeSH Terms

Computational Biology Ligands Protein Binding Protein Interaction Mapping/methods Proteins/chemistry,metabolism Software

Chemicals

Ligands Proteins

Authors & Affiliations

3 authors, click to expand affiliations / ORCID

Liu Shiyong

Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA.

Gao Ying

Vakser Ilya A

References (15)

15 references, click to expand

Development of unified statistical potentials describing protein-protein interactions.
Biophys J. 2003 Mar;84(3):1895-901 PMID: 12609891
From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent.
Proteins. 2007 Dec 1;69(4):697-8 PMID: 17912754
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.
Protein Sci. 2004 Apr;13(4):1043-55 PMID: 15044734
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2195-9 PMID: 1549581
Protein docking for low-resolution structures.
Protein Eng. 1995 Apr;8(4):371-7 PMID: 7567922
Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex.
Proteins. 1997;Suppl 1:226-30 PMID: 9485517
A systematic study of low-resolution recognition in protein--protein complexes.
Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8477-82 PMID: 10411900
PIBASE: a comprehensive database of structurally defined protein interfaces.
Bioinformatics. 2005 May 1;21(9):1901-7 PMID: 15657096
Development and testing of an automated approach to protein docking.
Proteins. 2005 Aug 1;60(2):296-301 PMID: 15981259
Protein-Protein Docking Benchmark 2.0: an update.
Proteins. 2005 Aug 1;60(2):214-6 PMID: 15981264
High-resolution protein-protein docking.
Curr Opin Struct Biol. 2006 Apr;16(2):183-93 PMID: 16546374
DOCKGROUND resource for studying protein-protein interfaces.
Bioinformatics. 2006 Nov 1;22(21):2612-8 PMID: 16928732
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures.
Nucleic Acids Res. 2007 Jan;35(Database issue):D575-9 PMID: 17071962
DOCKGROUND system of databases for protein recognition studies: unbound structures for docking.
Proteins. 2007 Dec 1;69(4):845-51 PMID: 17803215
Protein-protein docking: is the glass half-full or half-empty?
Trends Biotechnol. 2004 Mar;22(3):110-6 PMID: 15036860

Article Info

Journal

Bioinformatics (Oxford, England)

Abbr.

Bioinformatics

ISSN

1367-4811

DOI

10.1093/bioinformatics/btn497

Published

2008-11-15

Epub

2008-00-23

Pages

2634-5

Language

English

Region

England

NLM ID

9808944

PMCID

PMC2579708

Subset

Grants

NIGMS NIH HHS · R01 GM074255 · United States

External Links

PubMed source DOI: 10.1093/bioinformatics/btn497 PMC Full Text View journal details

Analysis Services

DOCKGROUND protein-protein docking decoy set.

Contact

WeChat Official Account