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SINAPs：一种用于分子动力学模拟相互作用网络分析与可视化的软件工具。

SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations.

作者信息

Bedart Corentin, Renault Nicolas, Chavatte Philippe, Porcherie Adeline, Lachgar Abderrahim, Capron Monique, Farce Amaury

机构信息

Univ. Lille, Inserm, CHU Lille, U1286 - Infinite - Institute for Translational Research in Inflammation, F-59000 Lille, France.

Par'Immune, Bio-incubateur Eurasanté, 70 rue du Dr. Yersin, 59120 Loos-Lez-Lille, France.

出版信息

J Chem Inf Model. 2022 Mar 28;62(6):1425-1436. doi: 10.1021/acs.jcim.1c00854. Epub 2022 Mar 3.

DOI:10.1021/acs.jcim.1c00854
PMID:35239339
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8966674/
Abstract

As long as the structural study of molecular mechanisms requires multiple molecular dynamics reflecting contrasted bioactive states, the subsequent analysis of molecular interaction networks remains a bottleneck to be fairly treated and requires a user-friendly 3D view of key interactions. Structural Interaction Network Analysis Protocols (SINAPs) is a proprietary python tool developed to (i) quickly solve key interactions able to distinguish two protein states, either from two sets of molecular dynamics simulations or from two crystallographic structures, and (ii) render a user-friendly 3D view of these key interactions through a plugin of UCSF Chimera, one of the most popular open-source viewing software for biomolecular systems. Through two case studies, glucose transporter-1 (GLUT-1) and A2A adenosine receptor (A2AR), SINAPs easily pinpointed key interactions observed experimentally and relevant for their bioactivities. This very effective tool was thus applied to identify the amino acids involved in the molecular enzymatic mechanisms ruling the activation of an immunomodulator drug candidate, P28 glutathione-S-transferase (P28GST). SINAPs is freely available at https://github.com/ParImmune/SINAPs.

摘要

只要分子机制的结构研究需要多个反映不同生物活性状态的分子动力学，那么随后对分子相互作用网络的分析仍然是一个有待妥善处理的瓶颈，并且需要对关键相互作用有一个用户友好的三维视图。结构相互作用网络分析协议（SINAPs）是一个专有的Python工具，其开发目的是：（i）快速解析能够区分两种蛋白质状态的关键相互作用，这两种状态可以来自两组分子动力学模拟，也可以来自两个晶体结构；（ii）通过UCSF Chimera（一种最流行的用于生物分子系统的开源可视化软件）的插件，呈现这些关键相互作用的用户友好的三维视图。通过葡萄糖转运蛋白-1（GLUT-1）和A2A腺苷受体（A2AR）这两个案例研究，SINAPs轻松地找出了实验观察到的、与其生物活性相关的关键相互作用。因此，这个非常有效的工具被用于识别参与调控免疫调节药物候选物P28谷胱甘肽-S-转移酶（P28GST）激活的分子酶促机制中的氨基酸。SINAPs可在https://github.com/ParImmune/SINAPs上免费获取。

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