ReviewNature protocols2022
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.
Review in Nature protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
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Who cites it
63 citing papers in PubMed.
- Mechanistical and structural basis of Kv channel inhibition by 4-aminopyridine.bioRxiv : the preprint server for biology · 2026Article
- Integrating Green Process Engineering With Whole-Cell Catalysis to Intensify Sustainable Glucaric Acid Production.Biotechnology and bioengineering · 2026Article
- Metadynamics Simulations Meet Ligand Design for the Reversible Inhibition of Human Peroxiredoxin 5.ACS omega · 2026Article
- How Medically Important Antimicrobials Bind to the 30S Ribosomal Subunit in a Bacterial Pathogen.Biochemistry · 2026Article
- Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological complexity.Nature communications · 2026Article
- Accelerating molecular dynamics simulations using fast Ewald summation with prolates.Nature communications · 2026Article
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- Article
- 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
- Prediction of Protein-Ligand Binding Affinities Using Atomic Surface Site Interaction Points.Journal of chemical information and modeling · 2026Article
- Article
- Fine-Tuning Side Chain Substitutions: Impacts on the Lipophilicity-Solubility-Permeability Interplay in Macrocyclic Peptides.Marine drugs · 2025Article
- MnM-W-MMGBSA: A Computational Strategy to Improve Relative Binding Free Energies of Protein-Protein Interaction Systems.The journal of physical chemistry. B · 2025Article
- Degradation of polyethylene terephthalate by microorganisms and their enzymes: A review of experimental and in silico research.World journal of microbiology & biotechnology · 2025Review
- Article
- Benchmarking Alchemical Relative Binding Free Energy Calculations for Nucleotide Binding to Multimeric ATPases.Journal of chemical theory and computation · 2025Article
- On Free Energy Calculations in Drug Discovery.Accounts of chemical research · 2025Article
- Molecular dynamics simulations of proteins: an in-depth review of computational strategies, structural insights, and their role in medicinal chemistry and drug development.Biological cybernetics · 2025Review
- Discovery of a potent ROR1 inhibitor using μs-scale MD simulations, wt-metadynamics, and absolute binding free energy calculations.Journal of molecular modeling · 2025Article
- clusttraj: A Solvent-Informed Clustering Tool for Molecular Modeling.Journal of chemical theory and computation · 2025Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Designing a reliable computational methodology to calculate protein:ligand standard binding free energies is extremely challenging. The large change in configurational enthalpy and entropy that accompanies the association of ligand and protein is notoriously difficult to capture in naive brute-force simulations. Addressing this issue, the present protocol rests upon a rigorous statistical mechanical framework for the determination of protein:ligand binding affinities together with the comprehensive Binding Free-Energy Estimator 2 (BFEE2) application software. With the knowledge of the bound state, available from experiments or docking, application of the BFEE2 protocol with a reliable force field supplies in a matter of days standard binding free energies within chemical accuracy, for a broad range of protein:ligand complexes. Limiting undesirable human intervention, BFEE2 assists the end user in preparing all the necessary input files and performing the post-treatment of the simulations towards the final estimate of the binding affinity.
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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.