RCSB 蛋白质数据库：通过全面的结构比对探索蛋白质 3D 相似性。

RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.

机构信息

Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, United States.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States.

出版信息

Bioinformatics. 2024 Jun 3;40(6). doi: 10.1093/bioinformatics/btae370.

DOI:10.1093/bioinformatics/btae370

PMID:38870521

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11212067/

Abstract

MOTIVATION

Tools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioinformatics, enabling visual exploration of evolutionary and functional relationships. However, the absence of a user-friendly, browser-based tool for creating alignments and visualizing them at both 1D sequence and 3D structural levels makes this process unnecessarily cumbersome.

RESULTS

We introduce a novel pairwise structure alignment tool (rcsb.org/alignment) that seamlessly integrates into the RCSB Protein Data Bank (RCSB PDB) research-focused RCSB.org web portal. Our tool and its underlying application programming interface (alignment.rcsb.org) empowers users to align several protein chains with a reference structure by providing access to established alignment algorithms (FATCAT, CE, TM-align, or Smith-Waterman 3D). The user-friendly interface simplifies parameter setup and input selection. Within seconds, our tool enables visualization of results in both sequence (1D) and structural (3D) perspectives through the RCSB PDB RCSB.org Sequence Annotations viewer and Mol* 3D viewer, respectively. Users can effortlessly compare structures deposited in the PDB archive alongside more than a million incorporated Computed Structure Models coming from the ModelArchive and AlphaFold DB. Moreover, this tool can be used to align custom structure data by providing a link/URL or uploading atomic coordinate files directly. Importantly, alignment results can be bookmarked and shared with collaborators. By bridging the gap between 1D sequence and 3D structures of proteins, our tool facilitates deeper understanding of complex evolutionary relationships among proteins through comprehensive sequence and structural analyses.

AVAILABILITY AND IMPLEMENTATION

The alignment tool is part of the RCSB PDB research-focused RCSB.org web portal and available at rcsb.org/alignment. Programmatic access is available via alignment.rcsb.org. Frontend code has been published at github.com/rcsb/rcsb-pecos-app. Visualization is powered by the open-source Mol* viewer (github.com/molstar/molstar and github.com/molstar/rcsb-molstar) plus the Sequence Annotations in 3D Viewer (github.com/rcsb/rcsb-saguaro-3d).

摘要

动机

用于蛋白质 3D 结构之间两两比对的工具对于结构生物学和生物信息学至关重要，可实现进化和功能关系的可视化探索。然而，由于缺乏一个用户友好的基于浏览器的工具来创建比对并在 1D 序列和 3D 结构水平上进行可视化，使得这一过程变得非常繁琐。

结果

我们引入了一种新的两两结构比对工具（rcsb.org/alignment），它无缝集成到 RCSB 蛋白质数据库（RCSB PDB）以研究为重点的 RCSB.org 网络门户中。我们的工具及其底层应用程序编程接口（alignment.rcsb.org）使用户能够通过访问已建立的比对算法（FATCAT、CE、TM-align 或 Smith-Waterman 3D），将几个蛋白质链与参考结构进行比对。用户友好的界面简化了参数设置和输入选择。在几秒钟内，我们的工具通过 RCSB PDB RCSB.org Sequence Annotations 查看器和 Mol* 3D 查看器分别在序列（1D）和结构（3D）视角下可视化结果。用户可以轻松地将 PDB 档案中存储的结构与来自 ModelArchive 和 AlphaFold DB 的超过 100 万个纳入的计算结构模型进行比较。此外，该工具还可以通过提供链接/URL 或直接上传原子坐标文件来对齐自定义结构数据。重要的是，比对结果可以被书签和与合作者共享。通过连接蛋白质的 1D 序列和 3D 结构，我们的工具通过全面的序列和结构分析，促进了对蛋白质之间复杂进化关系的更深入理解。

可用性和实现

该比对工具是 RCSB PDB 以研究为重点的 RCSB.org 网络门户的一部分，可在 rcsb.org/alignment 上使用。程序访问可通过 alignment.rcsb.org 获得。前端代码已在 github.com/rcsb/rcsb-pecos-app 上发布。可视化由开源 Mol* 查看器（github.com/molstar/molstar 和 github.com/molstar/rcsb-molstar）以及 3D 中的序列注释查看器（github.com/rcsb/rcsb-saguaro-3d）提供支持。