Context shapes

Efficient complementary shape matching for protein-protein docking

Zujun Shentu, Mohammad Al Hasan, Christopher Bystroff, Mohammed J. Zaki

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

We describe an efficient method for partial complementary shape matching for use in rigid protein-protein docking. The local shape features of a protein are represented using boolean data structures called Context Shapes. The relative orientations of the receptor and ligand surfaces are searched using precalculated lookup tables. Energetic quantities are derived from shape complementarity and buried surface area computations, using efficient boolean operations. Preliminary results indicate that our context shapes approach outperforms state-of-the-art geometric shape-based rigid-docking algorithms.

Original languageEnglish
Pages (from-to)1056-1073
Number of pages18
JournalProteins: Structure, Function and Genetics
Volume70
Issue number3
DOIs
Publication statusPublished - 15 Feb 2008
Externally publishedYes

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Proteins
Table lookup
Data structures
Ligands

Keywords

  • Local shape features
  • Protein docking
  • Protein shape matching
  • Protein surface representation

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

Context shapes : Efficient complementary shape matching for protein-protein docking. / Shentu, Zujun; Al Hasan, Mohammad; Bystroff, Christopher; Zaki, Mohammed J.

In: Proteins: Structure, Function and Genetics, Vol. 70, No. 3, 15.02.2008, p. 1056-1073.

Research output: Contribution to journalArticle

Shentu, Zujun ; Al Hasan, Mohammad ; Bystroff, Christopher ; Zaki, Mohammed J. / Context shapes : Efficient complementary shape matching for protein-protein docking. In: Proteins: Structure, Function and Genetics. 2008 ; Vol. 70, No. 3. pp. 1056-1073.
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