Efficient electrostatic solvation model for protein-fragment docking.

[Full text]1726/6857

Docking procedure

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Efficient electrostatic solvation model for protein-fragment docking.

Proteins. 2001 Feb 1;42(2):256-68

Authors: Majeux N, Scarsi M, Caflisch A

A method is presented for the fast evaluation of the binding energy of a protein-small molecule complex with electrostatic solvation. It makes use of a fast preprocessing step based on the assumption that the main contribution to electrostatic desolvation upon ligand binding originates from the displacement of the first shell of water molecules. For a rigid protein, the precomputation of the energy contributions on a set of grids allows the estimation of the energy in solution of about 300 protein-fragment binding modes per second on a personal computer. The docking procedure is applied to five rigid binding sites whose size ranges from 17 residues to a whole protein of 107 amino acids. Using a library of 70 mainly rigid molecules, known micromolar inhibitors or close analogs are docked and prioritized correctly. The docking based rank-ordering of the library requires about 5 h and is proposed as a complementary approach to structure-activity relationships by nuclear magnetic resonance. Proteins 2001;42:256-268.

PMID: 11119650 [PubMed - indexed for MEDLINE]

[Full text]1726/6857

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