PGR: A Graph Repository of Protein 3D-Structures

TL;DR

PGR is a comprehensive database transforming protein 3D-structures into graph representations, enabling advanced graph-based analysis and similarity search for bioinformatics research.

Contribution

It introduces a novel, publicly accessible repository of protein graphs with tools for conversion, visualization, and similarity search, bridging graph mining and protein structure analysis.

Findings

Contains graph representations of all known PDB proteins

Provides online conversion and visualization tools

Includes pre-computed graph attributes and similarity search

Abstract

Graph theory and graph mining constitute rich fields of computational techniques to study the structures, topologies and properties of graphs. These techniques constitute a good asset in bioinformatics if there exist efficient methods for transforming biological data into graphs. In this paper, we present Protein Graph Repository (PGR), a novel database of protein 3D-structures transformed into graphs allowing the use of the large repertoire of graph theory techniques in protein mining. This repository contains graph representations of all currently known protein 3D-structures described in the Protein Data Bank (PDB). PGR also provides an efficient online converter of protein 3D-structures into graphs, biological and graph-based description, pre-computed protein graph attributes and statistics, visualization of each protein graph, as well as graph-based protein similarity search tool. Such repository presents an enrichment of existing online databases that will help bridging the gap between graph mining and protein structure analysis. PGR data and features are unique and not included in any other protein database. The repository is available at http://wjdi.bioinfo.uqam.ca/.