Assessing protein-ligand interaction scoring functions with the CASF-2013 benchmark
Assessing protein-ligand interaction scoring functions with the CASF-2013 benchmark
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DOI：
10.1038/nprot.2017.114
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发表时间：
2018-04-01
期刊：
影响因子：
14.8
通讯作者：
Wang, Renxiao
中科院分区：
文献类型：
--
作者：
Li, Yan;Su, Minyi;Wang, Renxiao
评分函数是一组广泛应用于基于结构的药物设计的计算方法，用于快速评估蛋白质与配体的相互作用。迄今为止，基于不同的假设或算法，已经开发了一整套评分函数。因此，客观地评估评分功能的性能对最终用户和评分功能的开发人员都很重要。我们开发了评分函数比较评估（CASF）基准，作为评分函数评估的开放获取解决方案。最新的CASF-2013基准可以通过在不同蛋白质分子及其小分子配体之间形成的195个复合物的高质量测试集来评估给定评分函数的所谓“核心能力”、“排名能力”、“对接能力”和“筛选能力”。给出了几个主流软件程序（包括Schrodinger、MOE、Discovery Studio、SYBYL、GOLD）实现的标准评分函数的评价结果，供参考。自从第一次发布以来，这个基准就在评分函数社区中很受欢迎。在本协议中，我们提供了CASF-2013包中包含的数据文件的详细描述，以及如何使用包中包含的现成计算机脚本进行性能测试的分步说明。该协议有望降低CASF-2013基准的新老用户面前的技术障碍。在标准的桌面工作站上，一旦所需的输入，即在测试集上计算的结果准备好使用，完成一个评分功能的整个评估过程大约需要半个小时。
Scoring functions are a group of computational methods widely applied in structure-based drug design for fast evaluation of protein-ligand interactions. To date, a whole spectrum of scoring functions have been developed based on different assumptions or algorithms. Therefore, it is important to both the end users and the developers of scoring functions that their performance be objectively assessed. We have developed the comparative assessment of scoring functions (CASF) benchmark as an open-access solution for scoring function evaluation. The latest CASF-2013 benchmark enables evaluation of the so-called 'coring power', 'ranking power', 'docking power', and 'screening power' of a given scoring function with a high-quality test set of 195 complexes formed between diverse protein molecules and their small-molecule ligands. Evaluation results of the standard scoring functions implemented in several mainstream software programs (including Schrodinger, MOE, Discovery Studio, SYBYL, and GOLD) are provided as reference. This benchmark has become popular among the scoring function community since its first release. In this protocol, we provide detailed descriptions of the data files included in the CASF-2013 package and step-by-step instructions on how to conduct the performance tests with the ready-to-use computer scripts included in the package. This protocol is expected to lower the technical hurdles in front of new and existing users of the CASF-2013 benchmark. On a standard desktop workstation, it takes roughly half an hour to complete the whole evaluation procedure for one scoring function, once the required inputs, i.e., the results computed on the test set, are ready to use.