ChemFlow_py: a flexible toolkit for docking and rescoring

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Computer-Aided Molecular Design Pub Date : 2023-08-24 DOI:10.1007/s10822-023-00527-z

Luca Monari, Katia Galentino, Marco Cecchini

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Abstract

The design of accurate virtual screening tools is an open challenge in drug discovery. Several structure-based methods have been developed at different levels of approximation. Among them, molecular docking is an established technique with high efficiency, but typically low accuracy. Moreover, docking performances are known to be target-dependent, which makes the choice of the docking program and corresponding scoring function critical when approaching a new protein target. To compare the performances of different docking protocols, we developed ChemFlow_py, an automated tool to perform docking and rescoring. Using four protein systems extracted from DUD-E with 100 known active compounds and 3000 decoys per target, we compared the performances of several rescoring strategies including consensus scoring. We found that the average docking results can be improved by consensus ranking, which emphasizes the relevance of consensus scoring when little or no chemical information is available for a given target. ChemFlow_py is a free toolkit to optimize the performances of virtual high-throughput screening (vHTS). The software is publicly available at https://github.com/IFMlab/ChemFlow_py.

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ChemFlow_py:一个灵活的对接和记录工具包

精确的虚拟筛选工具的设计是药物发现中的一个公开挑战。几种基于结构的方法在不同的近似水平上得到了发展。其中，分子对接是一种成熟的技术，效率高，但精度低。此外，已知对接性能是目标依赖的，这使得对接程序的选择和相应的评分函数在接近新的蛋白质靶标时至关重要。为了比较不同对接协议的性能，我们开发了ChemFlow_py，这是一个自动执行对接和记录的工具。使用从ddu - e中提取的四种蛋白质系统，每个目标有100个已知活性化合物和3000个诱饵，我们比较了几种评分策略的性能，包括共识评分。我们发现，平均对接结果可以通过共识排序来改善，共识排序强调了在给定目标的化学信息很少或没有可用的情况下共识评分的相关性。ChemFlow_py是一个免费的工具包，用于优化虚拟高通量筛选(vHTS)的性能。该软件可在https://github.com/IFMlab/ChemFlow_py.Graphical abstract上公开获得

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来源期刊

Journal of Computer-Aided Molecular Design 生物-计算机：跨学科应用

CiteScore

8.00

自引率

8.60%

发文量

审稿时长

3 months

期刊介绍： The Journal of Computer-Aided Molecular Design provides a form for disseminating information on both the theory and the application of computer-based methods in the analysis and design of molecules. The scope of the journal encompasses papers which report new and original research and applications in the following areas: - theoretical chemistry; - computational chemistry; - computer and molecular graphics; - molecular modeling; - protein engineering; - drug design; - expert systems; - general structure-property relationships; - molecular dynamics; - chemical database development and usage.