xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures.

详细信息    查看全文

• 作者：Marco Pasi ; Matteo Tiberti ; Alberto Arrigoni ; Elena Papaleo
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2012
• 出版时间：July 23, 2012
• 年：2012
• 卷：52
• 期：7
• 页码：1865-1874
• 全文大小：535K
• 年卷期：v.52,no.7(July 23, 2012)
• ISSN：1549-960X

文摘

A versatile method to directly identify and analyze short- or long-range coupled or communicating residues in a protein conformational ensemble is of extreme relevance to achieve a complete understanding of protein dynamics and structural communication routes. Here, we present xPyder, an interface between one of the most employed molecular graphics systems, PyMOL, and the analysis of dynamical cross-correlation matrices (DCCM). The approach can also be extended, in principle, to matrices including other indexes of communication propensity or intensity between protein residues, as well as the persistence of intra- or intermolecular interactions, such as those underlying protein dynamics. The xPyder plugin for PyMOL 1.4 and 1.5 is offered as Open Source software via the GPL v2 license, and it can be found, along with the installation package, the user guide, and examples, at http://linux.btbs.unimib.it/xpyder/.