Data from: QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations
Data from: QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations
About this collection
- Extent
-
1 digital object.
- Description
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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
- Principal Investigator
- Funding
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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
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- Computational biophysics
- Computational chemistry
- Domain: Biological sciences
- Domain: Biomedical and clinical sciences
- Domain: Chemical sciences
- Domain: Information and computing sciences
- Drug-target kinetics
- Enhanced sampling
- Markovian milestoning
- Molecular dynamics
- Residence time
- Simulation-Enabled Estimation of Kinetic Rates version 2 (SEEKR2)
- Voronoi tessellations
Format
View formats within this collection
- Language
- English
- Identifier
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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
- 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
- QMrebind GitHub repository: https://github.com/seekrcentral/qmrebind
- SEEKR2 OpenMM Plugin GitHub repository: https://github.com/seekrcentral/seekr2
- Image source: Anupam Anand Ojha.
Primary associated publication
Software
Collection image
