ArticleJournal of chemical information and modeling2014
Analysis of factors influencing hydration site prediction based on molecular dynamics simulations.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Accelerated Hydration Site Localization and Thermodynamic Profiling.Journal of chemical information and modeling · 2025Article
- Marine-Derived Compounds as Potential Inhibitors of Hsp90 for Anticancer and Antimicrobial Drug Development: A Comprehensive In Silico Study.Molecules (Basel, Switzerland) · 2023Article
- Total free energy analysis of fully hydrated proteins.Proteins · 2023Article
- Instantaneous generation of protein hydration properties from static structures.Communications chemistry · 2020Article
- Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin.The journal of physical chemistry. B · 2019Article
- "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.Journal of computational chemistry · 2017Article
- Article
- Dissecting the Influence of Protein Flexibility on the Location and Thermodynamic Profile of Explicit Water Molecules in Protein-Ligand Binding.Journal of chemical theory and computation · 2016Article
- Current status and future prospects for enabling chemistry technology in the drug discovery process.F1000Research · 2016Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Water contributes significantly to the binding of small molecules to proteins in biochemical systems. Molecular dynamics (MD) simulation based programs such as WaterMap and WATsite have been used to probe the locations and thermodynamic properties of hydration sites at the surface or in the binding site of proteins generating important information for structure-based drug design. However, questions associated with the influence of the simulation protocol on hydration site analysis remain. In this study, we use WATsite to investigate the influence of factors such as simulation length and variations in initial protein conformations on hydration site prediction. We find that 4 ns MD simulation is appropriate to obtain a reliable prediction of the locations and thermodynamic properties of hydration sites. In addition, hydration site prediction can be largely affected by the initial protein conformations used for MD simulations. Here, we provide a first quantification of this effect and further indicate that similar conformations of binding site residues (RMSD < 0.5 Å) are required to obtain consistent hydration site predictions.
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Registered trials
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