Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Bioinformatics. 2017 Feb 1;33(3):444-446. doi: 10.1093/bioinformatics/btw638.
The recently released PyMod GUI integrates many of the individual steps required for protein sequence-structure analysis and homology modeling within the interactive visualization capabilities of PyMOL. Here we describe the improvements introduced into the version 2.0 of PyMod.
The original code of PyMod has been completely rewritten and improved in version 2.0 to extend PyMOL with packages such as Clustal Omega, PSIPRED and CAMPO. Integration with the popular web services ESPript and WebLogo is also provided. Finally, a number of new MODELLER functionalities have also been implemented, including SALIGN, modeling of quaternary structures, DOPE scores, disulfide bond modeling and choice of heteroatoms to be included in the final model.
PyMod 2.0 installer packages for Windows, Linux and Mac OS X and user guides are available at http://schubert.bio.uniroma1.it/pymod/index.html. The open source code of the project is hosted at https://github.com/pymodproject/pymod.
alessandro.paiardini@uniroma1.it or giacomo.janson@uniroma1.it
最近发布的 PyMod GUI 将蛋白质序列-结构分析和同源建模所需的许多单个步骤集成到 PyMOL 的交互式可视化功能中。在此，我们描述了 PyMod 2.0 版本中引入的改进。
PyMod 的原始代码在 2.0 版本中已被完全重写和改进，以将 Clustal Omega、PSIPRED 和 CAMPO 等软件包扩展到 PyMOL 中。还提供了与流行的网络服务 ESPript 和 WebLogo 的集成。最后，还实现了许多新的 MODELLER 功能，包括 SALIGN、四级结构建模、DOPE 评分、二硫键建模以及选择要包含在最终模型中的杂原子。
适用于 Windows、Linux 和 Mac OS X 的 PyMod 2.0 安装程序包以及用户指南可在 http://schubert.bio.uniroma1.it/pymod/index.html 上获得。该项目的开源代码托管在 https://github.com/pymodproject/pymod。
alessandro.paiardini@uniroma1.it 或 giacomo.janson@uniroma1.it
