Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.
Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
Proteins. 2020 Aug;88(8):1100-1109. doi: 10.1002/prot.25892. Epub 2020 Mar 25.
Integration of template-based modeling, global sampling and precise scoring is crucial for the development of molecular docking programs with improved accuracy. We combined template-based modeling and ab-initio docking protocol as hybrid docking strategy called CoDock for the docking and scoring experiments of the seventh CAPRI edition. For CAPRI rounds 38-45, we obtained acceptable or better models in the top 10 submissions for eight out of the 16 evaluated targets as predictors, nine out of the 16 targets as scorers. Especially, we submitted acceptable models for all of the evaluated protein-oligosaccharide targets. For the CASP13-CAPRI experiment (round 46), we obtained acceptable or better models in the top 5 submissions for 10 out of the 20 evaluated targets as predictors, 11 out of the 20 targets as scorers. The failed cases for our group were mainly the difficult targets and the protein-peptide systems in CAPRI and CASP13-CAPRI experiments. In summary, this CAPRI edition showed that our hybrid docking strategy can be efficiently adapted to the increasing variety of challenges in the field of molecular interactions.
整合基于模板的建模、全局采样和精确评分对于开发具有更高准确性的分子对接程序至关重要。我们将基于模板的建模和从头对接协议结合起来，形成一种名为 CoDock 的混合对接策略，用于第七届 CAPRI 版的对接和评分实验。在 CAPRI 第 38-45 轮中，我们的预测结果在 16 个评估目标中的 8 个目标中排名前 10，在 16 个目标中的 9 个目标中排名前 10，获得了可接受或更好的模型。特别是，我们为所有评估的蛋白质-寡糖目标提交了可接受的模型。在 CASP13-CAPRI 实验（第 46 轮）中，我们的预测结果在 20 个评估目标中的 10 个目标中排名前 5，在 20 个目标中的 11 个目标中排名前 5，获得了可接受或更好的模型。我们组失败的案例主要是 CAPRI 和 CASP13-CAPRI 实验中的困难目标和蛋白质-肽系统。总之，这一 CAPRI 版表明，我们的混合对接策略可以有效地适应分子相互作用领域不断增加的各种挑战。
