Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking.

Détails

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Accès restreint UNIL
Etat: Public
Version: Final published version
Licence: CC BY-NC-ND 4.0
ID Serval
serval:BIB_38F1AA57EFDC
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking.
Périodique
Journal of chemical information and modeling
Auteur⸱e⸱s
Röhrig U.F., Goullieux M., Bugnon M., Zoete V.
ISSN
1549-960X (Electronic)
ISSN-L
1549-9596
Statut éditorial
Publié
Date de publication
26/06/2023
Peer-reviewed
Oui
Volume
63
Numéro
12
Pages
3925-3940
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: ppublish
Résumé
Molecular docking is a computational approach for predicting the most probable position of a ligand in the binding site of a target macromolecule. Our docking algorithm Attracting Cavities (AC) has been shown to compare favorably to other widely used docking algorithms [Zoete, V.; et al. J. Comput. Chem. 2016, 37, 437]. Here we describe several improvements of AC, making the sampling more robust and providing more flexibility for either fast or high-accuracy docking. We benchmark the performance of AC 2.0 using the 285 complexes of the PDBbind Core set, version 2016. For redocking from randomized ligand conformations, AC 2.0 reaches a success rate of 73.3%, compared to 63.9% for GOLD and 58.0% for AutoDock Vina. Due to its force-field-based scoring function and its thorough sampling procedure, AC 2.0 also performs well for blind docking on the entire receptor surface. The accuracy of its scoring function allows for the detection of problematic experimental structures in the benchmark set. For cross-docking, the AC 2.0 success rate is about 30% lower than for redocking (42.5%), similar to GOLD (42.8%) and better than AutoDock Vina (33.1%), and it can be improved by an informed choice of flexible protein residues. For selected targets with a high success rate in cross-docking, AC 2.0 also achieves good enrichment factors in virtual screening.
Mots-clé
Molecular Docking Simulation, Ligands, Proteins/chemistry, Binding Sites, Algorithms, Protein Binding
Pubmed
Web of science
Données de la recherche
Création de la notice
08/06/2023 14:27
Dernière modification de la notice
24/10/2023 7:09
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