Protein–protein docking benchmark 2.0: An update

Citations Over TimeTop 10% of 2005 papers

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.

Related Papers

• → Pushing the accuracy limit of shape complementarity for protein-protein docking(2019)46 cited
• → DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking(2014)23 cited
• → Surface‐histogram: A new shape descriptor for protein‐protein docking(2011)17 cited
• → A New Pairwise Shape-Based Scoring Function to Consider Long-Range Interactions for Protein-Protein Docking(2017)9 cited
• → Computer Vision for Protein-protein Docking(2020)