Published February 27, 2023 | Version v2.0
Dataset Open

Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"

Authors/Creators

  • 1. School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, CH
  • 2. Chemistry Department, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, IT
  • 3. School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, CH. Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CH-1206, Geneva, CH. Chemistry Department, University College London (UCL), WC1E 6BT, London, UK. Swiss Bioinformatics Institute, University of Geneva, CH-1206, Geneva, CH

Description

Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints".

The directory is fully documented with README files.

Differences of V2.0 with V1.0:

  • Due to a software bug we had to re-parametrize the ligands whose torsions were parametized with ANI-2.X (ligand 6 and 7).
  • During the peer reviewing process we also parametrized with ANI-2.X and docked ligand 8.

Notes

V. Rizzi is acknowledged for useful discussions and help with manuscript revision. We acknowledge PRACE and the Swiss National Supercomputing Centre (CSCS) for large supercomputer time allocations on Piz Daint, project IDs: pr126, s1107, s1169, s1228. FLG acknowledges the Swiss National Science Foundation and Bridge for financial support (projects number: 200021_204795 and 40B2-0_203628). PP acknowledges the National Recovery and Resilience Plan, Mission 4 Component 2 - Investment 1.4 funded by the European Union - NextGenerationEU (CUP B83C22002830001).

Files

Supporting_Karrenbrock_et_al.zip

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Additional details

Related works

Is published in
Preprint: 10.26434/chemrxiv-2023-mc1gw (DOI)