A protein domain interaction interface database: InterPare

Reporter: Yu Lun KuoE-mail: sscc6991@gmail.comDate: May 22, 2007

Sungsam Gong1,2, Changbum Park3, Hansol Choi2, Junsu Ko7, Insoo Jang1, Jungsul Lee4, Dan M Bolser5, Donghoon Oh7, Deok-Soo Kim6 and Jong Bhak*1,8

Abstract

Rational drug Computational methods to identify the interaction

sites of lead compounds to the target moleculesIdentifying and classifying protein interaction

interfaces on a large scale can help researchers discover drug targets more efficiently.

Background

Protein structural interactomics to map all the protein domain interactions is becoming increasingly important As more complete genome sequences are made avail

able Higher resolution molecular interaction analysis

is also becoming more important

Background

There has been a new trend in the study of protein interfacesVoronoi diagram has been used to study interfaces

of protein complexes

Construction and Content

Interface identification methodsPSIMAPASAVoronoi

PSIMAP (Protein Structural Interactome)

Calculating the geometric distance between atoms in different domains

Two domains are assumed to interact with each otherAt least 5 residue pairs whose atomic distance falls

within 5 Angstrom distance (5-5 rule)The distance threshold (5 A is a default) can be

varied by users on the website

ASA (Accessible Surface Area)

ASA method detects protein regions that are buried and hence excluded from a solvent when forming a multimer or a complex

Define interface residues as residues that have lost more than 1 A solvent accessible surface area

ASA (Accessible Surface Area)

An interface region, in a domain Consists of at least 10 interface residues is acceptable, and t

hose having less than residues are considered as artifacts

All residues (Rid) in a SCOP domain and their corresponding residues (Rip) in a PDB entry

Voronoi Diagram

Power diagrams generate polygons which are bounded by edges

Marginal polygons need to be filtered outBecause those are irrelevant to the interacting

interfaces

http://www.cs.cornell.edu/Info/People/chew/Delaunay.html

•Between a domain and DNA (RNA)

•Between domain and non-domain

Utility

InterPare contains protein surface, interior, and interface information from PDB entries

Queries can beKeywordsPDB or SCOP IDsProtein sequences in FASTA format

http://interpare.net/