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A protein domain interaction interface database: InterPare

A protein domain interaction interface database: InterPare. 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. Reporter: Yu Lun Kuo E-mail: sscc6991@gmail.com Date: May 22, 2007. Abstract.

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A protein domain interaction interface database: InterPare

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  1. A protein domain interaction interface database: InterPare 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 Reporter: Yu Lun Kuo E-mail: sscc6991@gmail.com Date: May 22, 2007

  2. Abstract • Rational drug • Computational methods to identify the interaction sites of lead compounds to the target molecules • Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently.

  3. Background • Protein structural interactomics to map all the protein domain interactions is becoming increasingly important • As more complete genome sequences are made available • Higher resolution molecular interaction analysis is also becoming more important

  4. Background • There has been a new trend in the study of protein interfaces • Voronoi diagram has been used to study interfaces of protein complexes

  5. Construction and Content • Interface identification methods • PSIMAP • ASA • Voronoi

  6. PSIMAP (Protein Structural Interactome) • Calculating the geometric distance between atoms in different domains • Two domains are assumed to interact with each other • At 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

  7. 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

  8. ASA (Accessible Surface Area) • An interface region, in a domain • Consists of at least 10 interface residues is acceptable, and those having less than residues are considered as artifacts All residues (Rid) in a SCOP domain and their corresponding residues (Rip) in a PDB entry

  9. Voronoi Diagram • Power diagrams generate polygons which are bounded by edges • Marginal polygons need to be filtered out • Because those are irrelevant to the interacting interfaces • http://www.cs.cornell.edu/Info/People/chew/Delaunay.html

  10. Between a domain and DNA (RNA) • Between domain and non-domain

  11. Utility • InterPare contains protein surface, interior, and interface information from PDB entries • Queries can be • Keywords • PDB or SCOP IDs • Protein sequences in FASTA format

  12. http://interpare.net/

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