Qin Sanbo, Zhou Huan-Xiang
Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
Proteins. 2007 Dec 1;69(4):743-9. doi: 10.1002/prot.21752.
Docking of unbound protein structures into a complex has gained significant progress in recent years, but nonetheless still poses a great challenge. We have pursued a holistic approach to docking which brings together effective methods at different stages. First, protein-protein interaction sites are predicted or obtained from experimental studies in the literature. Interface prediction/experimental data are then used to guide the generation of docked poses or to rank docked poses generated from an unbiased search. Finally, selected models are refined by lengthy molecular dynamics (MD) simulations in explicit water. For CAPRI target T27, we used information on interaction sites as input to drive docking and as a filter to rank docked poses. Lead candidates were then clustered according to RMSD among them. From the clustering, 10 models were selected and subject to refinement by MD simulations. Our Model 7 is rated number one among all submissions according to L_rmsd. Six of our other submissions are rated acceptable. As scorer, eight of our submissions are rated acceptable.
近年来，将未结合的蛋白质结构对接至复合物中已取得显著进展，但仍然面临巨大挑战。我们采用了一种整体的对接方法，该方法在不同阶段整合了有效的方法。首先，预测蛋白质 - 蛋白质相互作用位点或从文献中的实验研究获取这些位点。然后，界面预测/实验数据用于指导对接姿势的生成，或对无偏向搜索生成的对接姿势进行排序。最后，通过在明确水环境中的长时间分子动力学（MD）模拟对选定的模型进行优化。对于CAPRI靶标T27，我们将相互作用位点的信息用作驱动对接的输入，并作为对对接姿势进行排序的筛选条件。然后根据候选领先模型之间的均方根偏差（RMSD）对它们进行聚类。从聚类中，选择了10个模型并通过MD模拟进行优化。根据L_rmsd，我们的模型7在所有提交的结果中排名第一。我们的其他六个提交结果被评为可接受。作为评分者，我们的八个提交结果被评为可接受。
