ReviewThe journal of physical chemistry. B2009
Computations of standard binding free energies with molecular dynamics simulations.
Review 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 221 papers.
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Who cites it
221 citing papers in PubMed.
- Binding of Anthracyclines Within DNA-Topoisomerase ΙΙ Cleavage Complexes: Thermodynamics and Interactions.Journal of chemical information and modeling · 2026Article
- An integrated computational strategy for profiling terpenoid for dual-target leads against Klebsiella pneumoniae penicillin-binding protein 3 and beta-lactamase.Molecular diversity · 2026Article
- Computational discovery of emodin-based anthraquinones as PARP-1 inhibitors with relevance to ovarian and prostate cancer.Scientific reports · 2026Article
- Efficient Binding Affinity Estimation for Fragment-Based Compounds Using a Separated Topologies Approach.Journal of chemical information and modeling · 2026Article
- Machine Learning-Driven Bioprospecting of Cholinergic Medicinal Plants for Putative Leads Against Butyrylcholinesterase Towards Alzheimer's Care.Biochemistry research international · 2026Article
- Molecular Dynamics-Based validation of a quinazoline-based KRAS inhibitor (C9) identified through QSAR-guided discovery.Frontiers in bioinformatics · 2026Article
- Distinct Target Site of Lenacapavir in Immature HIV-1 and Concurrent Binding with the Maturation Inhibitor Bevirimat.Journal of the American Chemical Society · 2025Article
- Reaction Engineering of In Vitro Natural Product Biosynthesis: Challenges and Strategies.Chembiochem : a European journal of chemical biology · 2025Review
- Exploring Artificial Intelligence's Potential to Enhance Conventional Anticancer Drug Development.Drug development research · 2025Review
- Thermodynamics and Kinetics of the Deintercalation of a Novel Anthracycline from Double-Stranded Oligonucleotide DNA.The journal of physical chemistry. B · 2025Article
- Binding Free Energy Calculations Based on the Path Collective Variable along a String Pathway.The journal of physical chemistry. B · 2025Article
- Article
- Binding Free Energy Analysis of Colicin D, E3 and E8 to Their Respective Cognate Immunity Proteins Using Computational Simulations.Molecules (Basel, Switzerland) · 2025Article
- Neural Network Potential with Multiresolution Approach Enables Accurate Prediction of Reaction Free Energies in Solution.Journal of the American Chemical Society · 2025Article
- A claudin5-binding peptide enhances the permeability of the blood-brain barrier in vitro.Science advances · 2025Article
- A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.Biophysics and physicobiology · 2025Article
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- Searching for Protein Off-Targets of Prostate-Specific Membrane Antigen-Targeting Radioligands in the Salivary Glands.Cancer biotherapy & radiopharmaceuticals · 2024Article
- Exploring PDK3 inhibition in lung cancer through drug repurposing for potential therapeutic interventions.Scientific reports · 2024Article
- Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.Journal of chemical theory and computation · 2024Article
161 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
An increasing number of studies have reported computations of the standard (absolute) binding free energy of small ligands to proteins using molecular dynamics (MD) simulations and explicit solvent molecules that are in good agreement with experiments. This encouraging progress suggests that physics-based approaches hold the promise of making important contributions to the process of drug discovery and optimization in the near future. Two types of approaches are principally used to compute binding free energies with MD simulations. The most widely known is the alchemical double decoupling method, in which the interaction of the ligand with its surroundings are progressively switched off. It is also possible to use a potential of mean force (PMF) method, in which the ligand is physically separated from the protein receptor. For both of these computational approaches, restraining potentials may be activated and released during the simulation for sampling efficiently the changes in translational, rotational, and conformational freedom of the ligand and protein upon binding. Because such restraining potentials add bias to the simulations, it is important that their effects be rigorously removed to yield a binding free energy that is properly unbiased with respect to the standard state. A review of recent results is presented, and differences in computational methods are discussed. Examples of computations with T4-lysozyme mutants, FKBP12, SH2 domain, and cytochrome P450 are discussed and compared. Remaining difficulties and challenges are highlighted.
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