ArticleJournal of chemical theory and computation2021
On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
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- The flexible stalk domain of sTREM2 modulates its interactions with brain-based phospholipids.eLife · 2025Article
- In search of a photoswitchable drug for serotonin receptors: a molecular dynamics simulation study.RSC advances · 2025Article
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- 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
- Structure optimization and molecular dynamics studies of new tumor-selectiveJournal of enzyme inhibition and medicinal chemistry · 2024Article
- StreaMD: the toolkit for high-throughput molecular dynamics simulations.Journal of cheminformatics · 2024Article
- Evaluation of an Affinity-Enhanced Anti-SARS-CoV2 Nanobody Design Workflow Using Machine Learning and Molecular Dynamics.Journal of chemical information and modeling · 2024Article
- Convergence criteria for single-step free-energy calculations: the relation between the Π bias measure and the sample variance.Chemical science · 2024Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular mechanics combined with Poisson-Boltzmann or generalized Born and solvent-accessible area solvation energies (MM/PBSA and MM/GBSA) are popular methods to estimate the free energy for the binding of small molecules to biomacromolecules. However, the estimation of the entropy has been problematic and time-consuming. Traditionally, normal-mode analysis has been used to estimate the entropy, but more recently, alternative approaches have been suggested. In particular, it has been suggested that exponential averaging of the electrostatic and Lennard-Jones interaction energies may provide much faster and more accurate entropies, the interaction entropy (IE) approach. In this study, we show that this exponential averaging is extremely poorly conditioned. Using stochastic simulations, assuming that the interaction energies follow a Gaussian distribution, we show that if the standard deviation of the interaction energies (σ
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Registered trials
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