SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations

Sun Zhaoxi; He Qiaole; Li XiaoZhu Zhengdan

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SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations

机译：SAMPL6 主客机结合亲和力和来自球坐标偏置仿真的绑定姿态

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titleAbstract/titlepHost–guest binding is a challenging problem in computer simulation. The prediction of binding affinities between hosts and guests is an important part of the statistical assessment of the modeling of proteins and ligands (SAMPL) challenges. In this work, the volume-based variant of well-tempered metadynamics is employed to calculate the binding affinities of the host–guest systems in the SAMPL6 challenge. By biasing the spherical coordinates describing the relative position of the host and the guest, the initial-configuration-induced bias vanishes and all possible binding poses are explored. The agreement between the predictions and the experimental results and the observation of new binding poses indicate that the volume-based technique serves as a nice candidate for the calculation of binding free energies and the search of the binding poses./p

机译：摘要主客结合是计算机仿真中一个具有挑战性的问题。预测宿主和客体之间的结合亲和力是蛋白质和配体建模（SAMPL）挑战统计评估的重要组成部分。在这项工作中，采用基于体积的回火元动力学变体来计算 SAMPL6 挑战中主-客体系统的结合亲和力。通过偏置描述主机和来宾相对位置的球面坐标，初始配置引起的偏置消失了，并探索了所有可能的绑定姿势。预测结果与实验结果的一致性以及对新结合位姿的观察表明，基于体积的技术是计算结合自由能和搜索结合位姿的良好候选者。

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来源
《Journal of Computer-Aided Molecular Design》 |2020年第5期|589-600|共12页
作者
Sun Zhaoxi; He Qiaole; Li XiaoZhu Zhengdan;
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作者单位

Computational Biomedicine (IAS-5/INM-9);

School of Biotechnology;

Physics, Engineering, Earth, Environment, Mechanics (PhITEM)CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica;

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原文格式 PDF
正文语种英语
中图分类电子计算机在化学中的应用;结构化学;
关键词
Free energy calculation; Binding pose; Binding affinity; Spherical coordinates; SAMPL6;

机译：自由能计算;绑定姿势;结合亲和力;球面坐标;SAMPL6的;

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SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations

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