ArticleJournal of computational chemistry2020
On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.
Article in Journal of computational chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Data-Efficient Equivariant NNPs Enable DFT-Accurate Simulations and Implicit Solvation Free Energies.The journal of physical chemistry. B · 2025Article
- DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations.Journal of chemical information and modeling · 2025Article
- Ligand Reorganization for End-Point Binding Free Energy Calculations: Identifying Preferred Poses of Fentanyls in the μ Opioid Receptor.Journal of chemical theory and computation · 2025Article
- Conserved Conformational Dynamics Reveal a Key Dynamic Residue in the Gatekeeper Loop of Human Cyclophilins.The journal of physical chemistry. B · 2023Article
- Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.Journal of chemical theory and computation · 2022Article
- On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies.Journal of chemical theory and computation · 2021Article
- Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS).Journal of chemical information and modeling · 2020Article
- Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions.Frontiers in physics · 2020Article
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Authors and funding
3 authors.
Funding
Abstract
The impact of harmonic restraints on protein heavy atoms and ligand atoms on end-point free energy calculations is systematically characterized for 54 protein-ligand complexes. We observe that stronger restraints reduce the equilibration time and statistical inefficiency, suppress conformational sampling, influence correlation with experiment, and monotonically decrease the estimated loss of entropy upon binding, leading to stronger estimated binding free energies in most systems. A statistical estimator that reweights for the biasing potential and includes data prior to the estimated equilibration time has the highest correlation with experiment. A spring constant of 20 cal mol
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