ArticleThe journal of physical chemistry. B2009
Prediction of the water content in protein binding sites.
Article in The journal of physical chemistry. B, 2009. 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.
- Predicting water at the protein interface in cryo-EM structures from MD-excess chemical potential.Biophysical journal · 2026Article
- 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
- 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
- A Guide to In Silico Drug Design.Pharmaceutics · 2022Review
- Absolute Binding Free Energy Calculations for Buried Water Molecules.Journal of chemical theory and computation · 2022Article
- Predicting Protein-Ligand Docking Structure with Graph Neural Network.Journal of chemical information and modeling · 2022Review
- Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.Journal of chemical theory and computation · 2022Article
- The oxytocin signaling complex reveals a molecular switch for cation dependence.Nature structural & molecular biology · 2022Article
- Plasticity in ligand recognition at somatostatin receptors.Nature structural & molecular biology · 2022Article
- Predicting Conserved Water Molecules in Binding Sites of Proteins Using Machine Learning Methods and Combining Features.Computational and mathematical methods in medicine · 2022Article
- Article
- Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies.Journal of computer-aided molecular design · 2021Article
- Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo.Journal of computer-aided molecular design · 2021Article
- Accurate Prediction of Hydration Sites of Proteins Using Energy Model With Atom Embedding.Frontiers in molecular biosciences · 2021Article
- GridSolvate: A Web Server for the Prediction of Biomolecular Hydration Properties.Journal of chemical information and modeling · 2020Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks.Journal of chemical information and modeling · 2020Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
An efficient molecular simulation methodology has been developed to determine the positioning of water molecules in the binding site of a protein or protein-ligand complex. Occupancies and absolute binding free energies of water molecules are computed using a statistical thermodynamics approach. The methodology, referred to as Just Add Water Molecules (JAWS), features "theta-water" molecules that can appear and disappear on a binding-site grid. Key approximations render the technique far more efficient than conventional free energy simulations. Testing of JAWS on five diverse examples (neuraminidase, scytalone dehydratase, major urinary protein 1, beta-lactoglobulin, and COX-2) demonstrates its accuracy in locating hydration sites in comparison to results from high-resolution crystal structures. Possible applications include aid in refinement of protein crystal structures, drug lead optimization, setup of docking calculations, and simulations of protein-ligand complexes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.