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pyProGA-A PyMOL plugin for protein residue network analysis.

Authors :
Sladek V
Yamamoto Y
Harada R
Shoji M
Shigeta Y
Sladek V
Source :
PloS one [PLoS One] 2021 Jul 30; Vol. 16 (7), pp. e0255167. Date of Electronic Publication: 2021 Jul 30 (Print Publication: 2021).
Publication Year :
2021

Abstract

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.<br />Competing Interests: The authors have declared that no competing interests exist.

Details

Language :
English
ISSN :
1932-6203
Volume :
16
Issue :
7
Database :
MEDLINE
Journal :
PloS one
Publication Type :
Academic Journal
Accession number :
34329304
Full Text :
https://doi.org/10.1371/journal.pone.0255167