ArticleJournal of computational chemistry2018
Power transformations improve interpolation of grids for molecular mechanics interaction energies.
Article in Journal of computational chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Precomputed grid potential (PGP) method: Exact reciprocal-space acceleration of particle mesh Ewald for Monte Carlo simulations.The Journal of chemical physics · 2026Article
- 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
- GridFF: Efficient Simulation of Organic Molecules on Rigid Substrates.Journal of chemical theory and computation · 2025Article
- Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.Journal of computational chemistry · 2020Article
- Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 : Binding free energies between flexible ligands and rigid receptors.Journal of computer-aided molecular design · 2019Article
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Abstract
A common strategy for speeding up molecular docking calculations is to precompute nonbonded interaction energies between a receptor molecule and a set of three-dimensional grids. The grids are then interpolated to compute energies for ligand atoms in many different binding poses. Here, I evaluate a smoothing strategy of taking a power transformation of grid point energies and inverse transformation of the result from trilinear interpolation. For molecular docking poses from 85 protein-ligand complexes, this smoothing procedure leads to significant accuracy improvements, including an approximately twofold reduction in the root mean square error at a grid spacing of 0.4 Å and retaining the ability to rank docking poses even at a grid spacing of 0.7 Å. © 2018 Wiley Periodicals, Inc.
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