ReviewJournal of chemical theory and computation2023
Alchemical Free Energy Calculations on Membrane-Associated Proteins.
Review in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Is the Bilayer Insertion of the Peptide KALP23 Under Kinetic or Thermodynamic Control?The Journal of membrane biology · 2026Article
- Docking of virtual libraries identifies small-molecule agonists of neurotensin receptors with analgesic activity.Nature communications · 2026Article
- NEMAT: An Automated Nonequilibrium Free-Energy Framework for Predicting Ligand Affinity in Membrane Proteins.Journal of chemical information and modeling · 2026Article
- A Systematic Benchmark Study of Free Energy Methods for Quantifying Light-Responsive Binding Affinities of Photoswitchable Antagonists of Beta-Adrenergic Receptors.Journal of medicinal chemistry · 2026Article
- BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA.Journal of chemical theory and computation · 2026Article
- Ultra-large virtual screening unveils potent agonists of the neuromodulatory orphan receptor GPR139.Nature communications · 2025Article
- The molecular mechanisms of visual chromophore release from cellular retinaldehyde-binding protein.Structure (London, England : 1993) · 2025Article
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- A quantitative analysis of ligand binding at the protein-lipid bilayer interface.Communications chemistry · 2025Article
- Template-based modeling of insect odorant receptors outperforms AlphaFold3 for ligand binding predictions.Scientific reports · 2024Article
- Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.Journal of chemical information and modeling · 2024Article
- Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions.The journal of physical chemistry. B · 2024Article
- Alchemical Enhanced Sampling with Optimized Phase Space Overlap.Journal of chemical theory and computation · 2024Article
- Correlation of Experimental and Calculated Inhibition Constants of Protease Inhibitor Complexes.International journal of molecular sciences · 2024Article
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Authors and funding
13 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein-ligand and protein-lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein-lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.
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