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Mapping Protein Domain Interactions: InterPare Database for Rational Drug Design

The InterPare database facilitates the identification and classification of protein interaction interfaces to aid researchers in discovering drug targets efficiently. Utilizing advanced computational methods like PSIMAP and Voronoi diagrams, InterPare provides insights into protein domain interactions, using geometric distance metrics and solvent-accessible surface area analysis to define interactive sites. With access to detailed structural information from PDB entries, scientists can query data using PDB or SCOP IDs and FASTA formatted protein sequences, enhancing their understanding of protein interactions.

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Mapping Protein Domain Interactions: InterPare Database for Rational Drug Design

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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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