pyProGA-A PyMOL plugin for protein residue network analysis.

The field of protein residue network (PRN) research has brought several useful methods and techniques for structural analysis of proteins and protein complexes. Many of these are ripe and ready to be used by the proteomics community outside of the PRN specialists. In this paper we present software w...

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Autores principales:	Vladimir Sladek, Yuta Yamamoto, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9d94944a09e04cc5836c04ae64a61672
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spelling	oai:doaj.org-article:9d94944a09e04cc5836c04ae64a616722021-12-02T20:08:52ZpyProGA-A PyMOL plugin for protein residue network analysis.1932-620310.1371/journal.pone.0255167https://doaj.org/article/9d94944a09e04cc5836c04ae64a616722021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0255167https://doaj.org/toc/1932-6203The field of protein residue network (PRN) research has brought several useful methods and techniques for structural analysis of proteins and protein complexes. Many of these are ripe and ready to be used by the proteomics community outside of the PRN specialists. In this paper we present software which collects an ensemble of (network) methods tailored towards the analysis of protein-protein interactions (PPI) and/or interactions of proteins with ligands of other type, e.g. nucleic acids, oligosaccharides etc. In parallel, we propose the use of the network differential analysis as a method to identify residues mediating key interactions between proteins. We use a model system, to show that in combination with other, already published methods, also included in pyProGA, it can be used to make such predictions. Such extended repertoire of methods allows to cross-check predictions with other methods as well, as we show here. In addition, the possibility to construct PRN models from various kinds of input is so far a unique asset of our code. One can use structural data as defined in PDB files and/or from data on residue pair interaction energies, either from force-field parameters or fragment molecular orbital (FMO) calculations. pyProGA is a free open-source software available from https://gitlab.com/Vlado_S/pyproga.Vladimir SladekYuta YamamotoRyuhei HaradaMitsuo ShojiYasuteru ShigetaVladimir SladekPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0255167 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Vladimir Sladek Yuta Yamamoto Ryuhei Harada Mitsuo Shoji Yasuteru Shigeta Vladimir Sladek pyProGA-A PyMOL plugin for protein residue network analysis.
description	The field of protein residue network (PRN) research has brought several useful methods and techniques for structural analysis of proteins and protein complexes. Many of these are ripe and ready to be used by the proteomics community outside of the PRN specialists. In this paper we present software which collects an ensemble of (network) methods tailored towards the analysis of protein-protein interactions (PPI) and/or interactions of proteins with ligands of other type, e.g. nucleic acids, oligosaccharides etc. In parallel, we propose the use of the network differential analysis as a method to identify residues mediating key interactions between proteins. We use a model system, to show that in combination with other, already published methods, also included in pyProGA, it can be used to make such predictions. Such extended repertoire of methods allows to cross-check predictions with other methods as well, as we show here. In addition, the possibility to construct PRN models from various kinds of input is so far a unique asset of our code. One can use structural data as defined in PDB files and/or from data on residue pair interaction energies, either from force-field parameters or fragment molecular orbital (FMO) calculations. pyProGA is a free open-source software available from https://gitlab.com/Vlado_S/pyproga.
format	article
author	Vladimir Sladek Yuta Yamamoto Ryuhei Harada Mitsuo Shoji Yasuteru Shigeta Vladimir Sladek
author_facet	Vladimir Sladek Yuta Yamamoto Ryuhei Harada Mitsuo Shoji Yasuteru Shigeta Vladimir Sladek
author_sort	Vladimir Sladek
title	pyProGA-A PyMOL plugin for protein residue network analysis.
title_short	pyProGA-A PyMOL plugin for protein residue network analysis.
title_full	pyProGA-A PyMOL plugin for protein residue network analysis.
title_fullStr	pyProGA-A PyMOL plugin for protein residue network analysis.
title_full_unstemmed	pyProGA-A PyMOL plugin for protein residue network analysis.
title_sort	pyproga-a pymol plugin for protein residue network analysis.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/9d94944a09e04cc5836c04ae64a61672
work_keys_str_mv	AT vladimirsladek pyprogaapymolpluginforproteinresiduenetworkanalysis AT yutayamamoto pyprogaapymolpluginforproteinresiduenetworkanalysis AT ryuheiharada pyprogaapymolpluginforproteinresiduenetworkanalysis AT mitsuoshoji pyprogaapymolpluginforproteinresiduenetworkanalysis AT yasuterushigeta pyprogaapymolpluginforproteinresiduenetworkanalysis AT vladimirsladek pyprogaapymolpluginforproteinresiduenetworkanalysis
_version_	1718375139721084928

pyProGA-A PyMOL plugin for protein residue network analysis.

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