Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding

By T. Young, Robert Abel, Byungchan Kim, B. Berne, Richard A. Friesner. Proceedings of the National Academy of Sciences of the United States of America, 2007

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Binding Affinity via Docking: Fact and Fiction (2018, methodology): “Furthermore, not all regions within the binding sites are hydrated and occupied by water molecules [49,50].”
Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap (2013, neutral): “, 2007 [53] Streptavidin, DB3, COX-2 Binding affinity (Y) Abel et al.”
Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances (2014, methodology): “Approaches following the inhomogeneous solvation theory [43] include JAWS [21], WaterMap [22], and WATMD (Novartis), but also other methods have been developed such as 3D-RISM [17] and SZMAP [20].”
Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination (2019, methodology): “WaterMap[11], on the other hand, relies on 2 ns MD simulations on a fixed protein.”