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

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Standard

xPyder : a PyMOL plugin to analyze coupled residues and their networks in protein structures. / Pasi, Marco; Tiberti, Matteo; Arrigoni, Alberto; Papaleo, Elena.

I: Journal of Chemical Information and Modeling, Bind 52, Nr. 7, 2012, s. 1865-1874.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Pasi, M, Tiberti, M, Arrigoni, A & Papaleo, E 2012, 'xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures', Journal of Chemical Information and Modeling, bind 52, nr. 7, s. 1865-1874. https://doi.org/10.1021/ci300213c

APA

Pasi, M., Tiberti, M., Arrigoni, A., & Papaleo, E. (2012). xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures. Journal of Chemical Information and Modeling, 52(7), 1865-1874. https://doi.org/10.1021/ci300213c

Vancouver

Pasi M, Tiberti M, Arrigoni A, Papaleo E. xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures. Journal of Chemical Information and Modeling. 2012;52(7):1865-1874. https://doi.org/10.1021/ci300213c

Author

Pasi, Marco ; Tiberti, Matteo ; Arrigoni, Alberto ; Papaleo, Elena. / xPyder : a PyMOL plugin to analyze coupled residues and their networks in protein structures. I: Journal of Chemical Information and Modeling. 2012 ; Bind 52, Nr. 7. s. 1865-1874.

Bibtex

@article{68960b393af84f2ab889d3147c05fdde,
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/.",
keywords = "Models, Molecular, Protein Conformation, Proteins, User-Computer Interface",
author = "Marco Pasi and Matteo Tiberti and Alberto Arrigoni and Elena Papaleo",
year = "2012",
doi = "10.1021/ci300213c",
language = "English",
volume = "52",
pages = "1865--1874",
journal = "Journal of Chemical Information and Modeling",
issn = "1549-9596",
publisher = "American Chemical Society",
number = "7",

}

RIS

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

Y1 - 2012

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

VL - 52

SP - 1865

EP - 1874

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

SN - 1549-9596

IS - 7

ER -

ID: 108138913