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Updated: Oct 22, 2025
Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
Published on: April 12, 2019
Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital
Iva Lukac1, Paul G Wyatt2, Ian H Gilbert1
1Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
None:
Water molecules play a crucial role in protein-ligand binding, and many tools exist that aim to predict the position and relative energies of these important, but challenging participants of biomolecular recognition. The available tools are, in general, capable of predicting the location of water molecules. However, predicting the effects of their displacement is still very challenging. In this work, a linear-scaling quantum mechanics-based approach was used to assess water network energetics and the changes in network stability upon ligand structural modifications. This approach offers a valuable way to improve understanding of SAR data and help guide compound design.
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