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Cited by 287

The DOI matches its Crossref record; 57 of the 57 references it cites were found in a registry or an index.

Docking Challenge: Protein Sampling and Molecular Docking Performance

Open access
Elokely, Khaled M., Doerksen, Robert J.·2013·Journal of Chemical Information and Modeling
DOI 10.1021/ci400040d
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Abstract

Computational tools are essential in the drug design process, especially in order to take advantage of the increasing numbers of solved X-ray and NMR protein-ligand structures. Nowadays, molecular docking methods are routinely used for prediction of protein-ligand interactions and to aid in selecting potent molecules as a part of virtual screening of large databases. The improvements and advances in computational capacity in the past decade have allowed for further developments in molecular docking algorithms to address more complicated aspects such as protein flexibility. The effects of incorporation of active site water molecules and implicit or explicit solvation of the binding site are other relevant issues to be addressed in the docking procedures. Using the right docking algorithm at the right stage of virtual screening is most important. We report a staged study to address the effects of various aspects of protein flexibility and inclusion of active site water molecules on docking effectiveness to retrieve (and to be able to predict) correct ligand poses and to rank docked ligands in relation to their biological activity for CHK1, ERK2, LpxC, and UPA. We generated multiple conformers for the ligand and compared different docking algorithms that use a variety of approaches to protein flexibility, including rigid receptor, soft receptor, flexible side chains, induced fit, and multiple structure algorithms. Docking accuracy varied from 1% to 84%, demonstrating that the choice of method is important.

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Metadata

Authors
Elokely, K. M., & Doerksen, R. J.
Venue
Journal of Chemical Information and Modeling
Publisher
American Chemical Society (ACS)
Published
2013-04-15
Volume
53
Issue
8
Pages
1934-1945
ISSN
  • 1549-9596 (ISSN-L)
  • 1549-960X
DOI
10.1021/ci400040d
OpenAlex
W2059921491
Cited by
287
References
57
FWCI
12.75
Type
journal article
Language
en
Open access
green

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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

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