10种分子对接程序采样和打分性能的综合测评
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- 英文论文题名：Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes:prediction accuracy of sampling power and scoring power
- 论文作者：王哲 ; 侯廷军
- 英文论文作者：Zhe Wang ; Tingjun Hou ; College of Pharmaceutical Sciences ; Zhejiang University
- 年：2016
- 作者机构：浙江大学药学院;
- 论文关键词：分子对接 ; 构象采样 ; 打分函数 ; 虚拟筛选
- 会议召开时间：2016-07-01
- 会议录名称：中国化学会第30届学术年会摘要集-第二十五分会：化学信息学与化学计量学
- 语种：中文
- 分类号：TQ460.1
- 学会代码：ZGHY
- 会议名称：中国化学会第30届学术年会-第二十五分会 ; 化学信息学与化学计量学
- 会议地点：中国辽宁大连
- 主办单位：中国化学会
- 学会名称：中国化学会
- 页数：1
- 文件大小：169k
- 原文格式：D
- 会议级别：全国
摘要
分子对接方法作为当今最为常用的基于结构的药物设计手段之一,其不仅能给出配体在靶标结合口袋内的正确结合模式,还可以预测两者的结合强度。随着分子对接程序的不断更新和开发,可选的程序越来越多,而对现有对接程序优缺点的全面了解则是能否将其合理应用于分子对接或基于分子对接的虚拟筛选研究中的前提条件。本课题基于PDBbind数据库中的2002个配体-蛋白晶体复合物,对包括五种商业化对接程序(LigandFit、Glide、GOLD、MOE Dock、Surflex-Dock)和五种学术免费的对接程序(AutoDock、AutoDock Vina、LeDock、rDock、UCSF DOCK)的采样性能和打分性能进行了系统的测评。
As one of the most popular computational approaches in modern structure-based drug design,molecular docking can be used not only to identify the correct conformation of a ligand within the target binding pocket but also to estimate the strength of interaction between target and ligand.Nowadays,as a variety of docking programs are available for the scientific community,a comprehensive understanding of advantages and limitations of each docking program is fundamentally important to conduct more reasonable docking studies and docking-based virtual screening.In the present study,based on an extensive dataset of 2002 protein-ligand complexes from PDBbind database(version 2014),the performance often docking programs,including five commercial programs(LigandFit,Glide,GOLD,MOE Dock,and Surflex-Dock) and five academic programs(AutoDock,AutoDock Vina,LeDock,rDock,and UCSF DOCK),was systematically evaluated by examining the accuracies of binding pose prediction(sampling power) and binding affinity estimation(scoring power).
As one of the most popular computational approaches in modern structure-based drug design,molecular docking can be used not only to identify the correct conformation of a ligand within the target binding pocket but also to estimate the strength of interaction between target and ligand.Nowadays,as a variety of docking programs are available for the scientific community,a comprehensive understanding of advantages and limitations of each docking program is fundamentally important to conduct more reasonable docking studies and docking-based virtual screening.In the present study,based on an extensive dataset of 2002 protein-ligand complexes from PDBbind database(version 2014),the performance often docking programs,including five commercial programs(LigandFit,Glide,GOLD,MOE Dock,and Surflex-Dock) and five academic programs(AutoDock,AutoDock Vina,LeDock,rDock,and UCSF DOCK),was systematically evaluated by examining the accuracies of binding pose prediction(sampling power) and binding affinity estimation(scoring power).
引文
[1]Wang,Z.;Sun,H.;Yao,X.;Li,D.;Xu,L.;Li,Y.;Tian,S.;Hou,T.Phys.Chem.Chem.Phys.,2016,DOI:10.1039/C6CP01555G