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Docking软件大比拼

已有 12247 次阅读 2009-12-10 03:02 |个人分类:科研笔记|系统分类:科研笔记

最近一直忙于一些软件的docking测试工具,目的是想了解下到底这些形形色色的对接软件效果如果。当然测试的结构大部分都是和自己课题相关的,基本上都是基于糖作为底物的对接测试,结果以与晶体结构的RMSD来作为衡量标准。先一起回顾下这些docking软件的基本小常识

Glide is a fast and accurate docking program that addresses a number of problems, ranging from fast database screening to highly accurate docking. The hierarchical filters in Glide ensure a fast and efficient reduction of large data sets to the few drug candidates that bind best with the target.

Gold is a genetic algorithm based method for ligand protein docking. It is distributed by the Cambridge Crystallographic Database.

MVD(Molegro Virtual Docker) is an integrated platform for predicting protein-ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity.

FlexX is a computer program for predicting protein-ligand interactions. For a protein with known three-dimensional structure and a small ligand molecule, FlexX predicts the geometry of the protein-ligand complex and estimates the binding affinity. The two main applications of FlexX are complex prediction and virtual screening. Complex prediction is used, when you have a protein and a small molecule binding to it but no structure of the protein-ligand complex. FlexX can be used to create and rank a series of possible protein-ligand complexes. In virtual screening, you have a protein and a set of compounds and you are interested in prioritizing the compounds for experimental testing.


AutoDock is LGA(Lamarckian Genetic Algorithm) algorithm based suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. It is available for free for academics institutions and can be installed on most unix machines.

DOCK is a software that can examine possible binding orientations of protein-protein and protein- DNA complexes. It can be used to search databases of molecular structures for compounds which act as enzyme inhibitors or which bind to target receptors. It can also search databases for DNA-binding compounds. It is available for unix workstations and is free for academic users.

再来看看这些软件的内在算法和打分函数的情况:


之前在一些文献和一些软件的官方网站看到了别人做的一些docking测试的结果。比如有篇JMC Docking测试的结果如下:
MVD: 87%, Glide: 82%, Surflex: 75%, FlexX: 58%

在schrodinger的官方网站则有这样一组数据:




为了验证这些软件对自己所做课题的实用性,选取了Glide, MVD, Gold, Flexx作为测试对象,对于同一个晶体结构选择了多种类似底物作测试,整个Docking的测试数组大概是20对。虽然不然文献的测试样本那么多,但基本上每组测试结果都和总体的结果一致。就上述4个软件而言,精准度如下:

Glide>Gold>MVD>Flexx

可能测试的底物比较局限,结果会与全面测试有些出入,但至少对自己课题和与糖相关的课题而言,还是具体参考价值。值得指出的是:Glide对于比较大的分子,比如:含有3个环以上的糖,对接效果明显好于其他软件。Gold对于单糖和双糖的对接效果也是非常好的,与Glide相当。



http://blog.sciencenet.cn/blog-355217-277476.html

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