ArticlePloS one2022
PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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Who cites it
3 citing papers in PubMed.
- Are QM/MM models systematically improvable? A case study on carbonic anhydrase binding affinities.Journal of computer-aided molecular design · 2026Article
- Superwater as a generative AI framework to predict water molecule positions on protein structures.Communications chemistry · 2025Article
- The structure and dynamics of water molecule networks underlie catalytic efficiency in a glycoside exo-hydrolase.Communications biology · 2025Article
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Authors and funding
3 authors.
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Abstract
Water molecules at the protein-small molecule interface often form hydrogen bonds with both the small molecule ligand and the protein, affecting the structural integrity and energetics of a binding event. The inclusion of these 'bridging waters' has been shown to improve the accuracy of predicted docked structures; however, due to increased computational costs, this step is typically omitted in ligand docking simulations. In this study, we introduce a resource-efficient, Rosetta-based protocol named "PlaceWaters" to predict the location of explicit interface bridging waters during a ligand docking simulation. In contrast to other explicit water methods, this protocol is independent of knowledge of number and location of crystallographic waters in homologous structures. We test this method on a diverse protein-small molecule benchmark set in comparison to other Rosetta-based protocols. Our results suggest that this coarse-grained, structure-based approach quickly and accurately predicts the location of bridging waters, improving our ability to computationally screen drug candidates.
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