Data from: QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations
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Description
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 v.2 (SEEKR2) 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. Anupam Ojha acknowledges the support of the Molecular Sciences Software Institute (MolSSI) fellowship under NSF Grant OAC-1547580. Rommie Amaro acknowledges support from NSF Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS) CHE060063 and NIHGM132826. Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp) Ojha, Anupam A.; Votapka, 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
Type
dataset
Identifier
ark:/20775/bb6120206r
Language
English
Subject
Molecular dynamics Computational biophysics Voronoi tessellations Simulation-Enabled Estimation of Kinetic Rates version 2 (SEEKR2) Computational chemistry Residence time Enhanced sampling Drug-target kinetics Markovian milestoning
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