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Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples

Cite this: J. Chem. Inf. Model. 2018, 58, 8, 1625–1637
Publication Date (Web):July 23, 2018
https://doi.org/10.1021/acs.jcim.8b00271
Copyright © 2018 American Chemical Society

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    Abstract

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    Water molecules are of great importance for the correct representation of ligand binding interactions. Throughout the last years, water molecules and their integration into drug design strategies have received increasing attention. Nowadays a variety of tools are available to place and score water molecules. However, the most frequently applied software solutions require substantial computational resources. In addition, none of the existing methods has been rigorously evaluated on the basis of a large number of diverse protein complexes. Therefore, we present a novel method for placing water molecules, called WarPP, based on interaction geometries previously derived from protein crystal structures. Using a large, previously compiled, high-quality validation set of almost 1500 protein–ligand complexes containing almost 20 000 crystallographically observed water molecules in their active sites, we validated our placement strategy. We correctly placed 80% of the water molecules within 1.0 Å of a crystallographically observed one.

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    20. Wei Xiao, Juhui Ren, Jutao Hao, Haoyu Wang, Yuhao Li, Liangzhao Lin, . Predicting Conserved Water Molecules in Binding Sites of Proteins Using Machine Learning Methods and Combining Features. Computational and Mathematical Methods in Medicine 2022, 2022 , 1-11. https://doi.org/10.1155/2022/5104464
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    23. Balázs Zoltán Zsidó, Csaba Hetényi. The role of water in ligand binding. Current Opinion in Structural Biology 2021, 67 , 1-8. https://doi.org/10.1016/j.sbi.2020.08.002
    24. Ahmadreza Ghanbarpour, Amr H. Mahmoud, Markus A. Lill. Instantaneous generation of protein hydration properties from static structures. Communications Chemistry 2020, 3 (1) https://doi.org/10.1038/s42004-020-00435-5
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