Protein–protein docking benchmark 2.0: An update
- 24 June 2005
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 60 (2) , 214-216
- https://doi.org/10.1002/prot.20560
Abstract
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. Proteins 2005;60:214–216.Keywords
This publication has 7 references indexed in Scilit:
- SCOP: A structural classification of proteins database for the investigation of sequences and structuresPublished by Elsevier ,2006
- Atomic contact vectors in protein‐protein recognitionProteins-Structure Function and Bioinformatics, 2003
- A protein–protein docking benchmarkProteins-Structure Function and Bioinformatics, 2003
- ZDOCK: An initial‐stage protein‐docking algorithmProteins-Structure Function and Bioinformatics, 2003
- Assessment of blind predictions of protein–protein interactions: Current status of docking methodsProteins-Structure Function and Bioinformatics, 2003
- The Protein Data BankNucleic Acids Research, 2000
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997