Affiliation:
1. State Key Laboratory of Natural Medicines, Department of Chinese Medicine, Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
Abstract
Water plays a significant role in determining the protein–ligand binding modes, especially when water molecules are involved in mediating protein–ligand interactions, and these important water molecules are receiving more and more attention in recent years. Considering the effects of water molecules has gradually become a routine process for accurate description of the protein–ligand interactions. As a free docking program, Autodock has been most widely used in predicting the protein–ligand binding modes. However, whether the inclusion of water molecules in Autodock would improve its docking performance has not been systematically investigated. Here, we incorporate important bridging water molecules into Autodock program, and systematically investigate the effectiveness of these water molecules in protein–ligand docking. This approach was evaluated using 18 structurally diverse protein–ligand complexes, in which several water molecules bridge the protein–ligand interactions. Different treatment of water molecules were tested by using the fixed and rotatable water molecules, and a considerable improvement in successful docking simulations was found when including these water molecules. This study illustrates the necessity of inclusion of water molecules in Autodock docking, and emphasizes the importance of a proper treatment of water molecules in protein–ligand binding predictions.
Funder
National Natural Science Foundation of China
Publisher
World Scientific Pub Co Pte Lt
Subject
Computational Theory and Mathematics,Physical and Theoretical Chemistry,Computer Science Applications
Cited by
2 articles.
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1. Redocking the PDB;Journal of Chemical Information and Modeling;2023-12-18
2. The role of water in ligand binding;Current Opinion in Structural Biology;2021-04