School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA-30332, USA.
Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden.
Curr Opin Struct Biol. 2024 Dec;89:102922. doi: 10.1016/j.sbi.2024.102922. Epub 2024 Sep 26.
Residue interaction networks (RINs) provide graph-based representations of interaction networks within proteins, providing important insight into the factors driving protein structure, function, and stability relationships. There exists a wide range of tools with which to perform RIN analysis, taking into account different types of interactions, input (crystal structures, simulation trajectories, single proteins, or comparative analysis across proteins), as well as formats, including standalone software, web server, and a web application programming interface (API). In particular, the ability to perform comparative RIN analysis across protein families using "metaRINs" provides a valuable tool with which to dissect protein evolution. This, in turn, highlights hotspots to avoid (or target) for in vitro evolutionary studies, providing a powerful framework that can be exploited to engineer new proteins.
残基相互作用网络 (RINs) 为蛋白质内部的相互作用网络提供了基于图的表示形式，为深入了解驱动蛋白质结构、功能和稳定性关系的因素提供了重要的线索。目前有许多工具可以进行 RIN 分析，考虑了不同类型的相互作用、输入（晶体结构、模拟轨迹、单个蛋白质或蛋白质间的比较分析）以及格式，包括独立软件、网络服务器和网络应用程序编程接口 (API)。特别是，使用“元 RINs”对蛋白质家族进行比较 RIN 分析的能力为剖析蛋白质进化提供了一个有价值的工具。这反过来又突出了在体外进化研究中要避免（或针对）的热点，为设计新蛋白质提供了一个强大的框架。
