A Web Site for Detecting Protein Structural Domain Neighbours

A query protein structure is compared with the VAST program to a database of target structures from the PDB (PDB40, list of protein structures having less than 40% of identical residues: 19 500 structures version 2011). The threshold of the VAST program is lowered in order to find the largest possible number of structures having a local similarity with the query protein. The purpose of the web site is to define structural domains in the query protein using the recurrence of these locally similar substructures. (http://genome.jouy.inra.fr/domire/). The list of matches is subsequently sorted according to two criteria: the number of aligned residues by VAST is at least 40% of the number of residues of the target, and 80% of the target length is aligned including gaps of non aligned residues if less than 40. Besides this list, a residue-residue alignment of the structural neighbour on the amino acid sequence of the query protein is provided together with a 3D view of their superposition. The object of this sorting is to help in detecting remote homologues and isolated protein structures matching the domain structures of a protein.