FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations,Journal of Chemical Information and Modeling

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FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2021-09-14 , DOI: 10.1021/acs.jcim.1c00215
Stamatia Zavitsanou _{1,

2} , Alexandros Tsengenes ₁ , Michail Papadourakis ₁ , Giorgio Amendola ₃ , Alexios Chatzigoulas _{1,

2} , Dimitris Dellis ₄ , Sandro Cosconati ₃ , Zoe Cournia ₁

Affiliation

Relative binding free energy calculations in drug design are becoming a useful tool in facilitating lead binding affinity optimization in a cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual creation of large numbers of input files to set up, run, and analyze free energy simulations. In this Application Note, we describe FEPrepare, a novel web-based tool, which automates the setup procedure for relative binding FEP calculations for the dual-topology scheme of NAMD, one of the major MD engines, using OPLS-AA force field topology and parameter files. FEPrepare provides the user with all necessary files needed to run a FEP/MD simulation with NAMD. FEPrepare can be accessed and used at https://feprepare.vi-seem.eu/.

中文翻译：

FEPrepare：用于自动设置相对结合自由能计算的基于 Web 的工具

药物设计中的相对结合自由能计算正成为一种有用的工具，以经济和时间高效的方式促进先导结合亲和力优化。但是，它们受到技术挑战的限制，例如手动创建大量输入文件以设置、运行和分析自由能模拟。在本应用说明中，我们介绍了 FEPrepare，这是一种新型的基于 Web 的工具，它使用 OPLS-AA 力场拓扑和 NAMD（主要 MD 引擎之一）的双拓扑方案自动执行相对绑定 FEP 计算的设置程序。参数文件。FEPrepare 为用户提供使用 NAMD 运行 FEP/MD 模拟所需的所有必要文件。FEPrepare 可以在 https://feprepare.vi-seem.eu/ 上访问和使用。

更新日期：2021-09-27

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