Radusky Leandro G, Serrano Luis
Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain.
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Bioinformatics. 2022 Apr 12;38(8):2353-2355. doi: 10.1093/bioinformatics/btac072.
Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software has proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of structures of the same protein using FoldX, an established forcefield and modelling software. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module and an easy integration with the data analysis ecosystem of the python programming language.
pyFoldX rely on the FoldX software for energy calculations and modelling, which can be downloaded upon registration in http://foldxsuite.crg.eu/ and its licence is free of charge for academics. The pyFoldX library is open-source. Full details on installation, tutorials covering the library functionality and the scripts used to generate the data and figures presented in this paper are available at https://github.com/leandroradusky/pyFoldX.
Supplementary data are available at Bioinformatics online.
近年来，可用的结构数量有所增加，不仅包括新蛋白质的结构，还包括与不同分子和蛋白质结晶的同一蛋白质的结构。虽然蛋白质设计软件已被证明在设计和修饰蛋白质方面很成功，但它们对同一蛋白质结构之间的小构象差异也可能过于敏感。为了解决这个问题，我们在此引入pyFoldX，这是一个Python库，它允许使用FoldX（一种成熟的力场和建模软件）对同一蛋白质的结构进行综合分析。该库提供了处理同一蛋白质不同结构的新功能、改进的分子参数化模块以及与Python编程语言的数据分析生态系统的轻松集成。
pyFoldX依靠FoldX软件进行能量计算和建模，可在http://foldxsuite.crg.eu/注册后下载，其许可证对学术界免费。pyFoldX库是开源的。有关安装的完整详细信息、涵盖库功能的教程以及用于生成本文中的数据和图表的脚本，可在https://github.com/leandroradusky/pyFoldX获取
补充数据可在《生物信息学》在线版获取。
