ArticleJournal of chemical theory and computation2017
Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Linking biochemical and cellular efficacy of MERS coronavirus main protease inhibitors.ACS pharmacology & translational science · 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
- Linking biochemical and cellular efficacy of MERS coronavirus main protease inhibitors.bioRxiv : the preprint server for biology · 2026Article
- Accurate protein-ligand binding free energy estimation using QM/MM on multi-conformers predicted from classical mining minima.Communications chemistry · 2024Article
- PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model.Journal of chemical theory and computation · 2024Article
- Energy penalties enhance flexible receptor docking in a model cavity.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Temperature artifacts in protein structures bias ligand-binding predictions.Chemical science · 2021Article
- Implicit ligand theory for relative binding free energies: II. An estimator based on control variates.Journal of physics communications · 2020Article
- Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and Its Inhibitors.International journal of molecular sciences · 2020Article
- On the polarization of ligands by proteins.Physical chemistry chemical physics : PCCP · 2020Article
- The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.Journal of computer-aided molecular design · 2020Article
- Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.Journal of computational chemistry · 2020Article
- On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.Journal of computational chemistry · 2020Article
- Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.Journal of chemical theory and computation · 2019Article
- Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α.PloS one · 2019Article
- 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
- Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method.Journal of computer-aided molecular design · 2018Article
- Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles.Journal of chemical information and modeling · 2018Article
- Power transformations improve interpolation of grids for molecular mechanics interaction energies.Journal of computational chemistry · 2018Article
- Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands.Physical chemistry chemical physics : PCCP · 2018Article
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3 authors.
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Abstract
We demonstrate the feasibility of estimating protein-ligand binding free energies using multiple rigid receptor configurations. On the basis of T4 lysozyme snapshots extracted from six alchemical binding free energy calculations with a flexible receptor, binding free energies were estimated for a total of 141 ligands. For 24 ligands, the calculations reproduced flexible-receptor estimates with a correlation coefficient of 0.90 and a root-mean-square error of 1.59 kcal/mol. The accuracy of calculations based on Poisson-Boltzmann/surface area implicit solvent was comparable to that of previously reported free energy calculations.
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