PGR: Protein Graph Repository
Computational Processing of Protein Structures
PGR aims to explore the protein 3D-structure within a graph perspective where a protein is seen as a network of amino acids. PGR offers the following services:

Repository:

A public repository of graphs representing all protein 3D-structures of the Protein Data Bank. Visualization and topological discription are also available for each protein-graph.

PG-similarity:

Allows to perform pairwise comparison of a selected protein against the entire repository.

PG-converter:

Allows building graphs from protein 3D-structures (pdb files) based on several methods from the literature.
PGR v1.0: Latest Release Statistics
Based on PDB dated July 11, 2014
Number of currently holding proteins graphs 188 252
Number of unique proteins 3D-structures 94 126
Protein graphs based on CAlpha 94 126
Protein graphs based on All Atoms 94 126
1A6Z protein 3D-structure An example of a protein 3D-structure: the HFE (human) hemochromatosis protein (PDB-id:1A6Z). 1A6Z protein graph The HFE(human) hemochromatosis protein-graph. Amino acids represent the graph nodes. The graph was generated using CAlpha method and a minimum distance threshold of 7.0 Aº between CAlpha atoms for building links between graph nodes. 1A6Z protein graph The HFE(human) hemochromatosis protein-graph. Amino acids represent the graph nodes. The graph was generated using All Atoms method and a minimum distance threshold of 4.0 Aº between all pairs of atoms for building links between graph nodes. 1A6Z protein 3D-structure transformed to graph The HFE(human) hemochromatosis protein 3D-structure (PDB-id:1A6Z) and its corresponding graph.
1A6Z protein 3D-structure transformed to graph An example of two subgraphs corresponding to two recurrent substructures extracted from a dataset of 38 proteins (including the HFE(human) hemochromatosis protein) from the immunoglobin C1-set domains family. All the 38 proteins were transformed into graphs using PG-converter, then a frequent subgraph discovery was performed to discover recurrent substructures with a minimum support threshold of 30%. This example shows the mapping of both subgraphs on the original 3D-structure of the HFE(human) hemochromatosis protein.