ArticleJournal of computational chemistry2020
Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations.Journal of chemical information and modeling · 2024Article
- BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling.Nature communications · 2023Article
- Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.Journal of chemical information and modeling · 2023Article
- The maximal and current accuracy of rigorous protein-ligand binding free energy calculations.Communications chemistry · 2023Article
- To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough.Journal of chemical information and modeling · 2023Article
- Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure.Journal of computer-aided molecular design · 2022Article
- An open-source molecular builder and free energy preparation workflow.Communications chemistry · 2022Article
- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].Living journal of computational molecular science · 2022Article
- Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands.Journal of chemical theory and computation · 2021Article
- Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications.Journal of computer-aided molecular design · 2021Article
- Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints.Journal of chemical theory and computation · 2021Article
- Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation.Scientific reports · 2021Article
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.Journal of chemical theory and computation · 2020Article
- Best Practices for Alchemical Free Energy Calculations [Article v1.0].Living journal of computational molecular science · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Pairwise-based methods such as the free energy perturbation (FEP) method have been widely deployed to compute the binding free energy differences between two similar host-guest complexes. The calculated pairwise free energy difference is either directly adopted or transformed to absolute binding free energy for molecule rank ordering. We investigated, through both analytic derivations and simulations, how the selection of pairs in the experiment could impact the overall prediction precision. Our studies showed that (1) the estimated absolute binding free energy (
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Registered trials
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