PyProGA-A PyMOL plugin for protein residue network analysis.

Mitsuo Shoji,Ryuhei Harada,Yasuteru Shigeta,Yuta Yamamoto,Vladimir Sladek,Bostjan Kobe

doi:10.1371/journal.pone.0255167

Mitsuo Shoji, Ryuhei Harada + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0255167

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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.

Highlights

The science of protein residue network (PRN) models is being developed over almost three decades
This paper introduces pyProGA as a tool for analysis of static protein residue networks
The use example exhibits a subset of its capabilities, yet we believe the investigation of protein-protein interfaces is amongst it strongest features. The usefulness of this software is not limited to pyProGA—Plugin for PRN analysis protein-protein interactions

Summary

Introduction

The science of protein residue network (PRN) models is being developed over almost three decades. This may indicate that for the community it is appealing to have exact, qualitative and quantitative protein models to study their structure, topology and dynamics. There is a different genre of PIN—Protein Interaction Network research in which the protein is the node and interactions between proteins are studied at molecular, but not at residue level [2,3,4]. These are not the subject of this work

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