Vymětal Jiří, Jakubec David, Galgonek Jakub, Vondrášek Jiří
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic.
Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Praha 1, 118 00, Czech Republic.
Nucleic Acids Res. 2021 Jul 2;49(W1):W15-W20. doi: 10.1093/nar/gkab377.
Interactions among amino acid residues are the principal contributor to the stability of the three-dimensional structure of a protein. The Amino Acid Interactions (INTAA) web server (https://bioinfo.uochb.cas.cz/INTAA/) has established itself as a unique computational resource, which enables users to calculate the contribution of individual residues in a biomolecular structure to its total energy using a molecular mechanical scoring function. In this update, we describe major additions to the web server which help solidify its position as a robust, comprehensive resource for biomolecular structure analysis. Importantly, a new continuum solvation model was introduced, allowing more accurate representation of electrostatic interactions in aqueous media. In addition, a low-overhead pipeline for the estimation of evolutionary conservation in protein chains has been added. New visualization options were introduced as well, allowing users to easily switch between and interrelate the energetic and evolutionary views of the investigated structures.
氨基酸残基之间的相互作用是蛋白质三维结构稳定性的主要贡献因素。氨基酸相互作用（INTAA）网络服务器（https://bioinfo.uochb.cas.cz/INTAA/）已成为一种独特的计算资源，它使用分子力学评分函数，使用户能够计算生物分子结构中单个残基对其总能量的贡献。在本次更新中，我们描述了对该网络服务器的主要新增功能，这些功能有助于巩固其作为生物分子结构分析的强大、全面资源的地位。重要的是，引入了一种新的连续介质溶剂化模型，能够更准确地表示水性介质中的静电相互作用。此外，还添加了一个用于估计蛋白质链中进化保守性的低开销流程。还引入了新的可视化选项，允许用户轻松地在被研究结构的能量视图和进化视图之间切换并相互关联。
