3DPatch：快速 3D 结构可视化与残基守恒。

3DPatch: fast 3D structure visualization with residue conservation.

机构信息

Department of Bioinformatics, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, 166 10, Czech Republic.

Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 2, 128 43, Czech Republic.

出版信息

Bioinformatics. 2019 Jan 15;35(2):332-334. doi: 10.1093/bioinformatics/bty464.

DOI:10.1093/bioinformatics/bty464

PMID:29931189

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6330005/

Abstract

SUMMARY

Amino acid residues showing above background levels of conservation are often indicative of functionally significant regions within a protein. Understanding how the sequence conservation profile relates in space requires projection onto a protein structure, a potentially time-consuming process. 3DPatch is a web application that streamlines this task by automatically generating multiple sequence alignments (where appropriate) and finding structural homologs, presenting the user with a choice of structures matching their query, annotated with residue conservation scores in a matter of seconds.

AVAILABILITY AND IMPLEMENTATION

3DPatch is written in JavaScript and is freely available at http://www.skylign.org/3DPatch/. Mozilla Firefox, Google Chrome, and Safari web browsers are supported. Source code is available under MIT license at https://github.com/davidjakubec/3DPatch.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

氨基酸残基的保守性水平高于背景水平通常表明蛋白质中有功能重要的区域。要了解序列保守性图谱在空间中的关系，需要将其投射到蛋白质结构上，这是一个潜在的耗时过程。3DPatch 是一个网络应用程序，它通过自动生成多个序列比对（在适当的情况下）和查找结构同源物，简化了这项任务，为用户提供了匹配其查询的结构选择，并在几秒钟内用残基保守性评分对其进行注释。

可用性和实现

3DPatch 是用 JavaScript 编写的，可以在 http://www.skylign.org/3DPatch/ 免费获得。支持 Mozilla Firefox、Google Chrome 和 Safari 网络浏览器。源代码可在 MIT 许可证下在 https://github.com/davidjakubec/3DPatch 获得。