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Extent

1 digital object.

Cite This Work

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

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.

Creation Date

• 2021 to 2023

Date Issued

• 2023

Authors

• Ojha, Anupam A.
• Votapka, Lane W.

Principal Investigator

• Amaro, Rommie E.

Funding

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.

Topics

• Computational biophysics
• Computational chemistry
• Drug-target kinetics
• Enhanced sampling
• Markovian milestoning
• Molecular dynamics
• Residence time
• Simulation-Enabled Estimation of Kinetic Rates version 2 (SEEKR2)
• Voronoi tessellations

Formats

View formats within this collection

• data
• text

Language

• English

Identifier

Identifier: Anupam Anand Ojha: https://orcid.org/0000-0001-6588-3092

Identifier: Lane W. Votapka: https://orcid.org/0000-0002-0865-5867

Identifier: Rommie E. Amaro: https://orcid.org/0000-0002-9275-9553

Related Resources

Primary associated publication

• Ojha, A. A.; Votapka, L. W.; Amaro, R. E. (2023). QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem. Sci. 15:13159-13175. https://doi.org/10.1039/D3SC04195F
• 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. This content is a preprint and has not been peer-reviewed. https://doi.org/10.26434/chemrxiv-2023-s4n3r

Software

• QMrebind GitHub repository: https://github.com/seekrcentral/qmrebind
• SEEKR2 OpenMM Plugin GitHub repository: https://github.com/seekrcentral/seekr2

Collection image

• Image source: Anupam Anand Ojha.