Protein-protein docking using three-dimensional reduced representations and based on a genetic algorithm

Andy Becue, Nathalie Meurice, Laurence Leherte, Daniel P. Vercauteren

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

An original scoring function dedicated to the docking of biological macromolecules is implemented in complementarity research within an automated algorithm. As these systems involve complicated atomic structures, we use for each partner reduced representations obtained by topological analysis of electron density maps at medium resolution, and develop specific terms for the characterization of the intermolecular interactions including a geometric fit based on the knowledge in a statistical survey, an electronic interaction potential using an expression of modified Coulomb type, and a penalty score based on detection of steric clashes. To validate the strategy, we performed automated docking runs, based on genetic algorithms (GA) for various protein-protein complexes including enzyme-inhibitor and antibody-antigen. For most complexes, the GA-proposed fit solutions have rmsd values below 3Å relative to the native structures.

Original languageEnglish (US)
Title of host publicationModels, Mysteries and Magic of Molecules
Pages301-323
Number of pages23
StatePublished - 2008
Externally publishedYes
Event2006 5th International Indaba Workshop of the International Union of Crystallography - Berg-en-Dal, South Africa
Duration: Aug 20 2006Aug 25 2006

Other

Other2006 5th International Indaba Workshop of the International Union of Crystallography
CountrySouth Africa
CityBerg-en-Dal
Period8/20/068/25/06

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Keywords

  • Critical points
  • Crystallographic medium resolution
  • Docking
  • Electron density
  • Genetic algorithms
  • Macromolecular complementarity

ASJC Scopus subject areas

  • Surfaces and Interfaces

Cite this

Becue, A., Meurice, N., Leherte, L., & Vercauteren, D. P. (2008). Protein-protein docking using three-dimensional reduced representations and based on a genetic algorithm. In Models, Mysteries and Magic of Molecules (pp. 301-323)