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Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking
[article]
2019
bioRxiv
pre-print
Highly-coordinated water molecules are frequently an integral part of protein- protein and protein-ligand interfaces. We introduce an updated energy model that efficiently captures the energetic effects of these highly-coordinated water molecules on the surfaces of proteins. A two-stage protocol is developed in which polar groups arranged in geometries suitable for water placement are first identified, then a modified Monte Carlo simulation allows highly coordinated waters to emerge. This
doi:10.1101/618603
fatcat:jfxl2xhb4rhshmzy22drwyi4dy