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

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State: Public
Version: Final published version
License: CC BY-NC-ND 4.0
Serval ID
serval:BIB_38F1AA57EFDC
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking.
Journal
Journal of chemical information and modeling
Author(s)
Röhrig U.F., Goullieux M., Bugnon M., Zoete V.
ISSN
1549-960X (Electronic)
ISSN-L
1549-9596
Publication state
Published
Issued date
26/06/2023
Peer-reviewed
Oui
Volume
63
Number
12
Pages
3925-3940
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
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.
Keywords
Molecular Docking Simulation, Ligands, Proteins/chemistry, Binding Sites, Algorithms, Protein Binding
Pubmed
Web of science
Research datasets
Create date
08/06/2023 14:27
Last modification date
24/10/2023 7:09
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