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Bhak, Jong
KOrean GenomIcs Center(KOGIC)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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Using convex hulls to extract interaction interfaces from known structures

Cited 16 times inthomson ciCited 18 times inthomson ci
Title
Using convex hulls to extract interaction interfaces from known structures
Other Titles
Using convex hulls to extract interaction interfaces from known structures.
Author
Dafas, PanosBolser, DanGomoluch, JacekBhak, Jong HwaSchroeder, Michael
Keywords
EMTREE medical terms: algorithm; article; classification; computer interface; computer program; controlled study; convergent evolution; information processing; mathematical computing; principal component analysis; priority journal; Protein Data Bank; protein domain; protein family; protein protein interaction; protein structure
Issue Date
2004-07
Publisher
OXFORD UNIV PRESS
Citation
BIOINFORMATICS, v.20, no.10, pp.1486 - 1490
Abstract
Motivation: Protein interactions provide an important context for the understanding of function. Experimental approaches have been complemented with computational ones, such as PSIMAP, which computes domain-domain interactions for all multi-domain and multi-chain proteins in the Protein Data Bank (PDB). PSIMAP has been used to determine that superfamilies occurring in many species have many interaction partners, to show examples of convergent evolution through shared interaction partners and to uncover complexes in the interaction map. To determine an interaction, the original PSIMAP algorithm checks all residue pairs of any domain pair defined by classification systems such as SCOP. The computation takes several days for the PDB. The computation of PSIMAP has two shortcomings: first, the original PSIMAP algorithm considers only interactions of residue pairs rather than atom pairs losing information for detailed analysis of contact patterns. At the atomic level the original algorithm would take months. Second, with the superlinear growth of PDB, PSIMAP is not sustainable. Results: We address these two shortcomings by developing a family of new algorithms for the computation of domain-domain interactions based on the idea of bounding shapes, which are used to prune the search space. The best of the algorithms improves on the old PSIMAP algorithm by a factor of 60 on the PDB. Additionally, the algorithms allow a distributed computation, which we carry out on a farm of 80 Linux PCs. Overall, the new algorithms reduce the computation at atomic level from months to 20 min. The combination of pruning and distribution makes the new algorithm scalable and sustainable even with the superlinear growth in PDB
URI
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DOI
10.1093/bioinformatics/bth106
ISSN
1367-4803
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BME_Journal Papers
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