School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom.
Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
J Chem Inf Model. 2020 Apr 27;60(4):1917-1921. doi: 10.1021/acs.jcim.9b01158. Epub 2020 Mar 26.
ProtoCaller is a Python library distributed through Anaconda which automates relative protein-ligand binding free energy calculations in GROMACS. It links a number of popular specialized tools used to perform protein setup and parametrization, such as PDB2PQR, Modeller, and AmberTools. ProtoCaller supports commonly used AMBER force fields with additional cofactor parameters, and AM1-BCC is used to derive ligand charges. ProtoCaller also comes with an extensive PDB parser, an enhanced maximum common substructure algorithm providing improved ligand-ligand mapping, and a light GROMACS wrapper for running multiple molecular dynamics simulations. ProtoCaller is highly relevant to most researchers in the field of biomolecular simulation, allowing a customizable balance between automation and user intervention.
ProtoCaller 是一个通过 Anaconda 分发的 Python 库，它可以在 GROMACS 中自动进行相对蛋白质-配体结合自由能计算。它链接了许多用于进行蛋白质设置和参数化的流行专用工具，如 PDB2PQR、Modeller 和 AmberTools。ProtoCaller 支持常用的 AMBER 力场，并提供额外的辅助因子参数，使用 AM1-BCC 来推导配体电荷。ProtoCaller 还附带了一个广泛的 PDB 解析器、一个增强的最大公共子结构算法，提供了改进的配体-配体映射，以及一个轻量级的 GROMACS 包装器，用于运行多个分子动力学模拟。ProtoCaller 与生物分子模拟领域的大多数研究人员都密切相关，允许在自动化和用户干预之间进行自定义平衡。
