Carrillo-Tripp Mauricio, Montiel-García Daniel Jorge, Brooks Charles L, Reddy Vijay S
Biomolecular Diversity Laboratory, Unidad de Genómica Avanzada (Langebio) CINVESTAV, Irapuato, Mexico.
Biomolecular Diversity Laboratory, Unidad de Genómica Avanzada (Langebio) CINVESTAV, Irapuato, Mexico.
J Struct Biol. 2015 Apr;190(1):47-55. doi: 10.1016/j.jsb.2015.02.003. Epub 2015 Feb 16.
Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the φ-ψ Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu.
蛋白质-蛋白质相互作用的结构分析和可视化是一项具有挑战性的任务，因为很难轻易了解构成界面的残基所形成的所有接触的程度。就病毒而言，结构分析的要求更高，因为存在多个界面，而且在大多数情况下，这些界面由数百个属于多种相互作用衣壳蛋白的接触残基形成。CapsidMaps是一种交互式分析和可视化工具，旨在为结构病毒学领域提供帮助。它是作为φ-ψ Explorer的改进扩展而开发的，在此我们描述其设计和实现的细节。我们展示了对一种球形病毒的分析结果，以展示这种新工具的特性和实用性。CapsidMaps还通过计算相似性（S）分数，促进了对两个球形病毒颗粒之间四级相互作用的比较。该工具还可用于识别暴露于溶剂中的残基、定位抗原表位区域的过程中以及与核酸基因组相互作用形成衣壳内表面的残基。CapsidMaps是VIPERdb科学网关的一部分，可作为基于网络且符合跨浏览器标准的应用程序在http://viperdb.scripps.edu上免费获取。
