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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
chemical engineering
Docking challenge: Protein sampling and molecular docking performance
Journal of Chemical Information and Modeling, Volume 53, No. 8, Year 2013
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Description
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. © 2013 American Chemical Society.
Authors & Co-Authors
Elokely, Khaled M.
United States, University
University of Mississippi
Doerksen, Robert J.
United States, University
University of Mississippi
United States, University
University of Mississippi School of Pharmacy
Statistics
Citations: 181
Authors: 2
Affiliations: 2
Identifiers
Doi:
10.1021/ci400040d
ISSN:
15499596
Research Areas
Environmental