Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
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DOI：
10.1016/j.jmb.2015.07.016
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发表时间：
2015-09-25
影响因子：
5.6
通讯作者：
Weng Z
中科院分区：
文献类型：
--
作者：
Vreven T;Moal IH;Vangone A;Pierce BG;Kastritis PL;Torchala M;Chaleil R;Jiménez-García B;Bates PA;Fernandez-Recio J;Bonvin AM;Weng Z
我们提供了我们广泛使用的蛋白质-蛋白质对接和结合亲和力基准的更新和集成版本。这些基准由蛋白质-蛋白质复合体的非冗余、高质量结构及其组分的非结合结构组成。对接基准中增加了55个新的络合物，其中35个具有实验测量的结合亲和力。这些更新的对接和亲和度基准现在分别包含230个和179个条目。特别是，抗体-抗原复合体的数量显著增加，在对接和亲和基准中分别增加了67%和74%。我们在新的案例上测试了之前开发的对接和亲和力预测算法。仅考虑每个基准案例的前十个对接预测，对所有55个案例的预测准确率为38%，仅对32个刚体案例的预测准确率高达50%。预测的亲和力分数与实验结合能相关，总体r=0.52，对于刚性络合物r=0.72。
We present an updated and integrated version of our widely used protein-protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high quality structures of protein-protein complexes along with the unbound structures of their components. Fifty-five new complexes were added to the docking benchmark, 35 of which have experimentally-measured binding affinities. These updated docking and affinity benchmarks now contain 230 and 179 entries, respectively. In particular, the number of antibody-antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively. We tested previously developed docking and affinity prediction algorithms on the new cases. Considering only the top ten docking predictions per benchmark case, a prediction accuracy of 38% is achieved on all 55 cases, and up to 50% for the 32 rigid-body cases only. Predicted affinity scores are found to correlate with experimental binding energies up to r=0.52 overall, and r=0.72 for the rigid complexes.