ArticleJournal of computational chemistry2020
Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.
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 10 papers.
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Who cites it
10 citing papers in PubMed.
- Absolute Binding Free Energy Calculations between the SARS-CoV-2 Main Protease and 130 Drug Leads Using Implicit Ligand Theory.Journal of chemical information and modeling · 2026Article
- Binding Free Energies without Alchemy.ArXiv · 2026Article
- GridFF: Efficient Simulation of Organic Molecules on Rigid Substrates.Journal of chemical theory and computation · 2025Article
- Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning.Journal of chemical information and modeling · 2025Article
- Automated Adaptive Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning.Research square · 2024Article
- Learning Efficient, Collective Monte Carlo Moves with Variational Autoencoders.Journal of chemical theory and computation · 2022Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- Implicit ligand theory for relative binding free energies: II. An estimator based on control variates.Journal of physics communications · 2020Article
- The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.Journal of computer-aided molecular design · 2020Article
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Abstract
Alchemical Grid Dock (AlGDock) is open-source software designed to compute the binding potential of mean force-the binding free energy between a flexible ligand and a rigid receptor-for a small organic ligand and a biological macromolecule. Multiple BPMFs can be used to rigorously compute binding affinities between flexible partners. AlGDock uses replica exchange between thermodynamic states at different temperatures and receptor-ligand interaction strengths. Receptor-ligand interaction energies are represented by interpolating precomputed grids. Thermodynamic states are adaptively initialized and adjusted on-the-fly to maintain adequate replica exchange rates. In demonstrative calculations, when the bound ligand is treated as fully solvated, AlGDock estimates BPMFs with a precision within 4 kT in 65% and within 8 kT for 91% of systems. It correctly identifies the native binding pose in 83% of simulations. Performance is sometimes limited by subtle differences in the important configuration space of sampled and targeted thermodynamic states. © 2019 Wiley Periodicals, Inc.
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