Novoa Trinidad, Laplaza Rubén, Peccati Francesca, Fuster Franck, Contreras-García Julia
Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F-75005 Paris, France.
Laboratoire Jacques-Louis Lions, LJLL, Sorbonne Université, CNRS, F-75005 Paris, France.
J Chem Inf Model. 2023 Aug 14;63(15):4483-4489. doi: 10.1021/acs.jcim.3c00271. Epub 2023 Aug 3.
It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.
众所周知，蛋白质的活性和功能与其二级、三级和四级结构密切相关。它们的生物学作用由其构象灵活性和整体折叠所调节，而这又在很大程度上受复杂的非共价相互作用网络支配。由于蛋白质尺寸较大，对其非共价相互作用网络进行分析具有挑战性，但可以为构象变化的能量学、蛋白质 - 蛋白质以及蛋白质 - 配体相互作用提供见解。基于约化密度梯度的非共价相互作用（NCI）指数是检测生物系统中弱相互作用的成熟工具。在这项工作中，我们展示了一个基于网络的应用程序，将该指数的应用扩展到蛋白质，它只需要分子结构作为输入，并提供非共价相互作用的数量、类型和强度的映射。结构准备是自动化的，并且允许直接从PDB数据库导入，使得经验有限的生物信息学科学家也可以访问这个服务器（https://nciweb.dsi.upmc.fr）。本文介绍了该工具的快速概述和简要说明，并给出了一个示例应用。
