Dataset in support of the paper: BRD4: Quantum mechanical protein-ligand binding free energies using the full-protein DFT-based QM-PBSA method

Abstract

Electronic Supporting Information for Publication "BRD4: Quantum mechanical protein-ligand binding free energies using the full-protein DFT-based QM-PBSA method" in PCCP, published in Physical Chemistry Chemical Physics Fully quantum mechanical approaches to calculating protein-ligand free energies of binding have the potential to reduce empiricism and explicitly account for all physical interactions responsible for protein-ligand binding. In this study, we show a realistic test of the linear-scaling DFT-based QM-PBSA method to estimate quantum mechanical protein-ligand binding free energies for a set of ligands binding to the pharmaceutical drug-target bromodomain containing protein 4 (BRD4). We show that quantum mechanical QM-PBSA is a significant improvement over traditional MM-PBSA in terms of accuracy against experiment and ligand rank ordering and that the quantum and classical binding energies are converged to a similar degree. We test the interaction entropy and normal mode entropy correction terms to QM- and MM-PBSA. The data set contains input and output files for DFT calculations performed and outputs for MM-PBSA/GBSA and normal mode analysis calculations.

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