ArticleJournal of molecular modeling2014
Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.
Article in Journal of molecular modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 37 citations in OpenAlex.
- MnM-W-MMGBSA: A Computational Strategy to Improve Relative Binding Free Energies of Protein-Protein Interaction Systems.The journal of physical chemistry. B · 2025Article
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- Pseudouridine residues as substrates for serum ribonucleases.RNA (New York, N.Y.) · 2025Article
- How THC works: Explaining ligand affinity for, and partial agonism of, cannabinoid receptor 1.iScience · 2025Article
- Mutations responsible for the carbapenemase activity of SME-1.RSC advances · 2022Article
- ReliableJournal of chemical information and modeling · 2022Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings.Frontiers in chemistry · 2018Article
- Article
- Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study.Journal of chemical information and modeling · 2017Article
- The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.Expert opinion on drug discovery · 2015Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of water molecules mediating the interaction between the receptor and the ligand can be studied by considering a few water molecules as a part of the receptor. We extended previous methods by allowing for a variable number of water molecules in the binding site. The effect of displaced water molecules can also be considered within the MM/GBSA philosophy by calculating the affinities of binding-site water molecules, both before and after binding of the ligand. To obtain proper energies, both the water molecules and the ligand need then to be converted to non-interacting ghost molecules and a single-average approach (i.e., the same structures are used for bound and unbound states) based on the simulations of both the complex and the free receptor can be used to improve the precision. The only problem is to estimate the free energy of an unbound water molecule. With an experimental estimate of this parameter, promising results were obtained for our test case.
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