Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.

Détails

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Etat: Public
Version: Final published version
ID Serval
serval:BIB_2D11A0764FB8
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.
Périodique
Journal of Computational Chemistry
Auteur⸱e⸱s
Zoete V., Schuepbach T., Bovigny C., Chaskar P., Daina A., Röhrig U.F., Michielin O.
ISSN
1096-987X (Electronic)
ISSN-L
0192-8651
Statut éditorial
Publié
Date de publication
2016
Peer-reviewed
Oui
Volume
37
Numéro
4
Pages
437-447
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Résumé
Molecular docking is a computational approach for predicting the most probable position of ligands in the binding sites of macromolecules and constitutes the cornerstone of structure-based computer-aided drug design. Here, we present a new algorithm called Attracting Cavities that allows molecular docking to be performed by simple energy minimizations only. The approach consists in transiently replacing the rough potential energy hypersurface of the protein by a smooth attracting potential driving the ligands into protein cavities. The actual protein energy landscape is reintroduced in a second step to refine the ligand position. The scoring function of Attracting Cavities is based on the CHARMM force field and the FACTS solvation model. The approach was tested on the 85 experimental ligand-protein structures included in the Astex diverse set and achieved a success rate of 80% in reproducing the experimental binding mode starting from a completely randomized ligand conformer. The algorithm thus compares favorably with current state-of-the-art docking programs.
Mots-clé
Algorithms, Ligands, Molecular Docking Simulation, Proteins/chemistry, Thermodynamics
Pubmed
Web of science
Open Access
Oui
Création de la notice
29/01/2016 16:32
Dernière modification de la notice
20/08/2019 14:12
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