Sampled ΔH/Δλ and ΔH data from ABFE calculations of 10 ligands bound to Cyclophilin D
- 1. The University of Oxford, Department of Biochemistry, South Parks Road, Oxford, UK, OX1 3QU
- 2. Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach an de Riß, Germany
Description
Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"
Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands bound to Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike the other Cyclophilin D
dataset provided in this work, simulations for these ABFE calculations were carried out using hydrogen mass repartitioning (HMR). The MCL-1, HSP90, and PWWP1 also used HMR.
All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information.
Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders).
Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).