虚拟筛选
蛋白质-配体对接
对接(动物)
计算机科学
计算生物学
自动停靠
药物设计
药物发现
寻找对接的构象空间
配体(生物化学)
生物信息学
化学
结合位点
小分子
生物
计算化学
生物化学
受体
医学
基因
护理部
作者
Stefano Forli,Ruth Huey,Michael E. Pique,Michel F. Sanner,David S. Goodsell,Arthur J. Olson
出处
期刊:Nature Protocols
[Springer Nature]
日期:2016-04-14
卷期号:11 (5): 905-919
被引量:1638
标识
DOI:10.1038/nprot.2016.051
摘要
This protocol describes the use of the AutoDock suite for computational docking in the study of protein–ligand interactions. A number of methods are described ranging from basic docking of drug molecules to virtual screening using a large ligand library of chemical compounds. Computational docking can be used to predict bound conformations and free energies of binding for small-molecule ligands to macromolecular targets. Docking is widely used for the study of biomolecular interactions and mechanisms, and it is applied to structure-based drug design. The methods are fast enough to allow virtual screening of ligand libraries containing tens of thousands of compounds. This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction and docking with explicit hydration. The entire protocol will require ∼5 h.
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