ArticlePloS one2012
Rapid and accurate prediction and scoring of water molecules in protein binding sites.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Amino Acids Frequency and Interaction Trends: Comprehensive Analysis of Experimentally Validated Viral Antigen-Antibody Complexes.Molecular biotechnology · 2026Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- Evaluating the ciprofloxacin potentiation efficacy of repurposed drug flupentixol through efflux pump inhibition of pathogenic bacteria.Scientific reports · 2025Article
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- Ten quick tips to perform meaningful and reproducible molecular docking calculations.PLoS computational biology · 2025Article
- Enthalpic Classification of Water Molecules in Target-Ligand Binding.Journal of chemical information and modeling · 2024Article
- HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures.Journal of chemical information and modeling · 2024Article
- The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering.International journal of molecular sciences · 2023Review
- WaterKit: Thermodynamic Profiling of Protein Hydration Sites.Journal of chemical theory and computation · 2023Article
- Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics.Physical chemistry chemical physics : PCCP · 2023Article
- Water Networks in Complexes between Proteins and FDA-Approved Drugs.Journal of chemical information and modeling · 2023Article
- Anti-Alopecia Activity of Alkaloids Group from Noni Fruit against Dihydrotestosterone-Induced Male Rabbits and Its Molecular Mechanism: In Vivo and In Silico Studies.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data.Journal of chemical information and modeling · 2022Article
- Bioinsecticidal activity of actinomycete secondary metabolites against the acetylcholinesterase of the legume's insect pest Acyrthosiphon pisum: a computational study.Journal, genetic engineering & biotechnology · 2022Article
- Imidazole and nitroimidazole derivatives as NADH-fumarate reductase inhibitors: Density functional theory studies, homology modeling, and molecular docking.Journal of computational chemistry · 2022Article
- Predicting Protein-Ligand Docking Structure with Graph Neural Network.Journal of chemical information and modeling · 2022Review
- Scoring Functions for Protein-Ligand Binding Affinity Prediction using Structure-Based Deep Learning: A Review.Frontiers in bioinformatics · 2022Article
- Point-specific interactions of isovitexin with the neighboring amino acid residues of the hACE2 receptor as a targeted therapeutic agent in suppressing the SARS-CoV-2 influx mechanism.Journal of advanced veterinary and animal research · 2022Article
- SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction.Journal of computer-aided molecular design · 2022Article
- Predicting Conserved Water Molecules in Binding Sites of Proteins Using Machine Learning Methods and Combining Features.Computational and mathematical methods in medicine · 2022Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.
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