xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures

Marco Pasi; Matteo Tiberti; Alberto Arrigoni; Elena Papaleo

doi:10.1021/ci300213c

xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures

Marco Pasi, Matteo Tiberti, Alberto Arrigoni, Elena Papaleo

37 Citations (Scopus)

Abstract

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/.

Original language	English
Journal	Journal of Chemical Information and Modeling
Volume	52
Issue number	7
Pages (from-to)	1865-1874
Number of pages	10
ISSN	1549-9596
DOIs	https://doi.org/10.1021/ci300213c
Publication status	Published - 23 Jul 2012
Externally published	Yes

Keywords

Models, Molecular
Protein Conformation
Proteins
User-Computer Interface

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10.1021/ci300213c

Cite this

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title = "xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures",

abstract = "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/.",

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author = "Marco Pasi and Matteo Tiberti and Alberto Arrigoni and Elena Papaleo",

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doi = "10.1021/ci300213c",

language = "English",

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TY - JOUR

T1 - xPyder

T2 - a PyMOL plugin to analyze coupled residues and their networks in protein structures

AU - Pasi, Marco

AU - Tiberti, Matteo

AU - Arrigoni, Alberto

AU - Papaleo, Elena

PY - 2012/7/23

Y1 - 2012/7/23

N2 - 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/.

AB - 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/.

KW - Models, Molecular

KW - Protein Conformation

KW - Proteins

KW - User-Computer Interface

U2 - 10.1021/ci300213c

DO - 10.1021/ci300213c

M3 - Journal article

C2 - 22721491

SN - 1549-9596

VL - 52

SP - 1865

EP - 1874

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

IS - 7

ER -

xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures

Abstract

Keywords

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