| 引用本文: | 杨伟,吕强.基于pose共享的蛋白质-配体构象并行搜索算法[J].生物信息学,2014,12(3):157-161. |
| YANG Wei,LV Qiang.Protein-Ligand conformation parallel search method based on pose sharing[J].Chinese Journal of Bioinformatics,2014,12(3):157-161. |
|
| 摘要: |
| RosettaLigand使用多次启动对接协议的方式对蛋白质-配体复合物构象空间进行采样,在串行或并行的构象搜索实例之间并不共享采样信息。因此并行对接与串行对接相比仅仅是增加了对接的速度,并不能改善对接的性能。我们对Rosetta 3.4版中的RosettaLigand算法进行了修改,在并行的对接实例之间共享采样信息,以实现多个对接实例协同优化采样进程。在一个包含11个目标的测试集合上进行的测试表明,共享采样信息在大多数对接实验中显著地提高了近天然构象在候选结构集合中的比例,同时还降低了整个候选结构集合的平均能量。 |
| 关键词: 分子对接 构象搜索 pose共享 RosettaLigand |
| DOI：10.3969/j.issn.1672-5565.2014.03.01 |
| 分类号:TH133; TP183 |
| 基金项目:国家自然科学基金(61170125)资助。 |
|
| Protein-Ligand conformation parallel search method based on pose sharing |
|
YANG Wei1, LV Qiang2
|
|
(1.Department of Computer Science and Technology, Soochow University, Suzhou 215006, China; 2.Jiangsu Provincial Key Laboratory for Information Processing Technology, Soochow University, Suzhou 215006, China )
|
| Abstract: |
| RosettaLigand samples the protein-ligand complex conformation space using multi-restart docking protocol. The sampling information is not shared between different docking instances. Thus parallel docking is just faster but not necessarily better than the serial version. We modified the original RoesttaLigand algorithm in Rosetta v3.4, making the sampling information shared between all docking instances to improve the sampling process. Test results on a 11-target simulation set showed that sharing sampling could increase the proportion of natural-like structures in candidate structures and lower the average energy of candidate structures in most cases. |
| Key words: Molecular docking Conformation search Pose sharing RosettaLigand |
