Data from: QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

Ojha, Anupam A.; Author; https://orcid.org/0000-0001-6588-3092; Votapka, Lane W.; Contributor; https://orcid.org/0000-0002-0865-5867; Amaro, Rommie E.; Corresponding Author; https://orcid.org/0000-0002-9275-9553
0000-0003-1023-6124

The data set contains the files necessary to recalculate/reproduce the unbinding rates of ligands for the model host-guest systems and Hsp90-inhibitor complexes in the paper "QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations." The data contains the Simulation Enabled Estimation of Kinetic Rates (SEEKR) and QMrebind-reparameterized SEEKR2 simulations for model host-guest systems and Hsp90-inhibitor complexes with instructions to compute the drug-target unbinding rates in these complexes. 

Please cite as:
Ojha, Anupam A.; Lane W.; Amaro, Rommie E. (2023). Data from: QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. UC San Diego Library Digital Collections. https://doi.org/10.6075/J09Z9545
Corresponding author:
Rommie E. Amaro − University of California, San Diego, La Jolla, California 92093, United States; orcid.org/0000- 0002-9275-9553; Email: ramaro@ucsd.edu

Primary associated publication:

Ojha, Anupam A.; Lane W.; Amaro, Rommie E. QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. ChemRxiv. Cambridge: Cambridge Open Engage; 2023, Version 1. https://doi.org/10.26434/chemrxiv-2023-s4n3r

Instructions:

To recalculate/reproduce the unbinding rates of ligands for the model host-guest systems and Hsp90-inhibitor complexes, please follow the given steps:

1. Make sure the SEEKR2 program is installed by following the steps given on GitHub: 
(a) https://github.com/seekrcentral/seekr2
(b) https://github.com/seekrcentral/seekr2\_openmm\_plugin

2. Create a SEEKR2 conda environment and activate it.

3. Untar the downloaded JAK data and place it in any given directory. 

4. Go to the qmrebind\_data directory and find further instructions in the "instructions.txt" files in the  host\_guest\_complexes and hsp90\_inhibitor\_complexes folders.