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

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

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

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

Phoenix/Scottsdale, AZ

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	Models, Mysteries and Magic of Molecules
Pages	301-323
Number of pages	23
State	Published - Dec 1 2008
Event	2006 5th International Indaba Workshop of the International Union of Crystallography - Berg-en-Dal, South Africa Duration: Aug 20 2006 → Aug 25 2006

Publication series

Name	Models, Mysteries and Magic of Molecules

Other

Other	2006 5th International Indaba Workshop of the International Union of Crystallography
Country/Territory	South Africa
City	Berg-en-Dal
Period	8/20/06 → 8/25/06

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, DP 2008, Protein-protein docking using three-dimensional reduced representations and based on a genetic algorithm. in Models, Mysteries and Magic of Molecules. Models, Mysteries and Magic of Molecules, pp. 301-323, 2006 5th International Indaba Workshop of the International Union of Crystallography, Berg-en-Dal, South Africa, 8/20/06.

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AU - Meurice, Nathalie

AU - Leherte, Laurence

AU - Vercauteren, Daniel P.

PY - 2008/12/1

Y1 - 2008/12/1

N2 - 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.

AB - 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.

KW - Critical points

KW - Crystallographic medium resolution

KW - Docking

KW - Electron density

KW - Genetic algorithms

KW - Macromolecular complementarity

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BT - Models, Mysteries and Magic of Molecules

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

Abstract

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Other

Keywords

ASJC Scopus subject areas

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