Protein-protein docking benchmark version 4.0.
We updated our protein-protein docking benchmark to include complexes that became available since our previous release. As before, we only considered high-resolution complex structures that are nonredundant at the family-family pair level, for which the X-ray or NMR unbound structures of the constituent proteins are also available. Benchmark 4.0 adds 52 new complexes to the 124 cases of Benchmark 3.0, representing an increase of 42%. Thus, benchmark 4.0 provides 176 unbound-unbound cases that can be used for protein-protein docking method development and assessment. Seventeen of the newly added cases are enzyme-inhibitor complexes, and we found no new antigen-antibody complexes. Classifying the new cases according to expected difficulty for protein-protein docking algorithms gives 33 rigid body cases, 11 cases of medium difficulty, and 8 cases that are difficult. Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/.
Hwang
Howook
H
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Vreven
Thom
T
Janin
Joël
J
Weng
Zhiping
Z
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008956:Models, Chemical; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software
D011506:Proteins
J Mol Biol. 1995 Apr 7;247(4):536-40
7723011
Proteins. 2008 Nov 15;73(3):705-9
18491384
J Biol Chem. 2003 Jun 27;278(26):24062-71
12684499
J Proteome Res. 2010 May 7;9(5):2216-25
20329755
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
10592235
Proteins. 2005 Aug 1;60(2):214-6
15981264
Bioinformatics. 2008 Sep 1;24(17):1865-73
18591193
Nucleic Acids Res. 2002 Jan 1;30(1):264-7
11752311
Proteins. 2003 Jul 1;52(1):2-9
12784359
Curr Opin Struct Biol. 2010 Apr;20(2):180-6
20194014
Protein Eng. 2001 Feb;14(2):105-13
11297668
Nat Protoc. 2010 May;5(5):883-97
20431534
J Am Chem Soc. 2003 Feb 19;125(7):1731-7
12580598
Proteins. 2003 Jul 1;52(1):80-7
12784371
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W233-8
18442991
Proteins. 2007 Dec 1;69(4):845-51
17803215
Protein Eng. 1995 Apr;8(4):371-7
7567922
Proteins. 2003 Jul 1;52(1):51-67
12784368
Bioinformatics. 2004 Jan 1;20(1):45-50
14693807
Proteins. 2003 Jul 1;52(1):88-91
12784372
Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10930-5
16043700