Efficient electrostatic solvation model for protein-fragment docking.
Proteins
; 42(2): 256-68, 2001 Feb 01.
Article
en En
| MEDLINE
| ID: mdl-11119650
ABSTRACT
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;42256-268.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Proteínas Nucleares
/
Trombina
/
Proteínas Proto-Oncogénicas
/
Proteínas Quinasas Activadas por Mitógenos
/
Proteína 1A de Unión a Tacrolimus
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Proteins
Asunto de la revista:
BIOQUIMICA
Año:
2001
Tipo del documento:
Article
País de afiliación:
Suiza