benchmarking and analysis of protein docking performance in rosetta v3.2基准测试和分析的蛋白质对接在罗塞塔v3.2的表现.pdfVIP

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2 1 2 2 2 2 Sidhartha Chaudhury , Monica Berrondo , Brian D. Weitzner , Pravin Muthu , Hannah Bergman , Jeffrey J. Gray2* 1 Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America, 2 Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America Abstract RosettaDock has been increasingly used in protein docking and design strategies in order to predict the structure of protein-protein interfaces. Here we test capabilities of RosettaDock 3.2, part of the newly developed Rosetta v3.2 modeling suite, against Docking Benchmark 3.0, and compare it with RosettaDock v2.3, the latest version of the previous Rosetta software package. The benchmark contains a diverse set of 116 docking targets including 22 antibody-antigen complexes, 33 enzyme-inhibitor complexes, and 60 ‘other’ complexes. These targets were further classified by expected docking difficulty into 84 rigid-body targets, 17 medium targets, and 14 difficult targets. We carried out local docking perturbations for each target, using the unbound structures when available, in both RosettaDock v2.3 and v3.2. Overall the performances of RosettaDock v2.3 and v3.2 were similar. RosettaDock v3.2 achieved 56 docking funnels, compared to 49 in v2.3. A breakdown of docking performance by protein complex type shows that RosettaDock v3.2 achieved docking funnels for 63% of antibody-antigen targets, 62% of enzyme-inhibitor targets, and 35% of ‘other’ targets. In terms of docking difficulty, RosettaDock v3.2 achieved funnels for 58% of rigid-body targets, 30% of me