Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Rome, Italy.
Bioinformatics. 2021 Jun 16;37(10):1471-1472. doi: 10.1093/bioinformatics/btaa849.
The PyMod project is designed to act as a fully integrated interface between the popular molecular graphics viewer PyMOL, and some of the most frequently used tools for structural bioinformatics, e.g. BLAST, HMMER, Clustal, MUSCLE, PSIPRED, DOPE and MODELLER. Here we report its latest release, PyMod 3, which has been completely renewed with a graphical interface written in PyQt, to make it compatible with the most recent PyMOL versions, and has been extended with a large set of new functionalities compared to its predecessor, i.e. PyMod 2. Starting from the amino acid sequence of a target protein, users can take advantage of PyMod 3 to carry out all the steps of the homology modeling process (i.e. template searching, target-template sequence alignment, model building and quality assessment). Additionally, the integrated tools in PyMod 3 may also be used alone, in order to extend PyMOL with a wide range of capabilities. Sequence similarity searches, multiple sequence/structure alignment building, phylogenetic trees and evolutionary conservation analyses, domain parsing, single/multiple chains and loop modeling can be performed in the PyMod 3/PyMOL environment.
A cross-platform PyMod 3 installer package for Windows, Linux and Mac OS X and a complete user guide with tutorials, are available at https://github.com/pymodproject/pymod.
Supplementary data are available at Bioinformatics online.
PyMod 项目旨在成为流行的分子图形查看器 PyMOL 与一些最常用的结构生物信息学工具（例如 BLAST、HMMER、Clustal、MUSCLE、PSIPRED、DOPE 和 MODELLER）之间的完全集成接口。这里我们报告其最新版本 PyMod 3，它已完全更新为使用 PyQt 编写的图形界面，使其与最新的 PyMOL 版本兼容，并与前身 PyMod 2 相比扩展了大量新功能。从目标蛋白质的氨基酸序列开始，用户可以利用 PyMod 3 执行同源建模过程的所有步骤（即模板搜索、目标-模板序列比对、模型构建和质量评估）。此外，PyMod 3 中的集成工具也可以单独使用，以便用广泛的功能扩展 PyMOL。可以在 PyMod 3/PyMOL 环境中执行序列相似性搜索、多序列/结构比对构建、系统发育树和进化保守性分析、结构域解析、单/多链和环建模。
适用于 Windows、Linux 和 Mac OS X 的跨平台 PyMod 3 安装程序包以及带有教程的完整用户指南可在 https://github.com/pymodproject/pymod 上获得。
补充数据可在 Bioinformatics 在线获得。
