Protein-Protein Docking Benchmark 2.0: an update.
We present a new version of the Protein-Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound-unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound-unbound cases, with 52 rigid-body cases, 13 medium-difficulty cases, and 7 high-difficulty cases with substantial conformational change. In addition, we retained 12 antibody-antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2.
Mintseris
Julian
J
Boston University Bioinformatics Program, Boston, Massachusetts 02215, USA.
Wiehe
Kevin
K
Pierce
Brian
B
Anderson
Robert
R
Chen
Rong
R
Janin
Joël
J
Weng
Zhiping
Z
D000465:Algorithms; D000818:Animals; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D019281:Dimerization; D006801:Humans; D020407:Internet; D046911:Macromolecular Substances; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D040681:Structural Homology, Protein
D046911:Macromolecular Substances