Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening.
Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening.
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DOI：
10.1371/journal.pone.0155183
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Villarreal MA
中科院分区：
文献类型：
--
作者：
Quiroga R;Villarreal MA
Autodock维纳是一个非常受欢迎的，被高度引用的开源对接程序。在这里，我们提出了一个评分函数，我们称之为Vinardo（维纳RaDii优化）。Vinardo基于维纳，并通过一种新颖的方法在最先进的数据集上进行训练。我们发现，传统的方法来训练经验评分函数，使用线性回归来优化预测和实验结合亲和力的相关性，并不会产生具有最佳对接能力的函数。另一方面，在精心策划的训练数据集上进行评分，最小化和重新对接的组合使我们能够开发具有最佳对接性能的简化评分函数。本文概述了Vinardo评分函数的发展过程，重点介绍了其与维纳评分函数的不同之处，并比较了两种评分函数在评分、对接和虚拟筛选应用中的性能。对于分析的所有数据集，Vinardo在所有测试中均优于维纳。Vinardo评分函数在维纳的一个分支Smina中作为一个选项提供，它可以在GNU公共许可证v2.0下从http://smina.sf.net免费获得。预编译的二进制文件、源代码、文档和使用Smina运行Vinardo评分函数的教程都可以在同一个地址获得。
Autodock Vina is a very popular, and highly cited, open source docking program. Here we present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based on Vina, and was trained through a novel approach, on state of the art datasets. We show that the traditional approach to train empirical scoring functions, using linear regression to optimize the correlation of predicted and experimental binding affinities, does not result in a function with optimal docking capabilities. On the other hand, a combination of scoring, minimization, and re-docking on carefully curated training datasets allowed us to develop a simplified scoring function with optimum docking performance. This article provides an overview of the development of the Vinardo scoring function, highlights its differences with Vina, and compares the performance of the two scoring functions in scoring, docking and virtual screening applications. Vinardo outperforms Vina in all tests performed, for all datasets analyzed. The Vinardo scoring function is available as an option within Smina, a fork of Vina, which is freely available under the GNU Public License v2.0 from http://smina.sf.net. Precompiled binaries, source code, documentation and a tutorial for using Smina to run the Vinardo scoring function are available at the same address.