Data from: QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations
Readme
File Size |
|
File Format |
|
Description | Information about the data and further instructions for the usage of data. |
Simulation files for host-guest complexes
File Size |
|
File Format |
|
Simulation files for the Hsp90-inhibitor complexes
File Size |
|
File Format |
|
Scope And Content | On 2023-11-28, 3 folders were updated to include the most recent simulation runs: compound37, compound43, plot_rates. In addition, 5 folders missing from the original .zip file were added: compound1, compound2, compound8, compound10, compound31. |
Molecular dynamics simulation data for Hsp90-inhibitor complexes
File Size |
|
File Format |
|
- Collection
- 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
- Principal Investigator
- Technical Details
-
1. SEEKR2 : https://github.com/seekrcentral/seekr2
2. qmrebind: https://github.com/seekrcentral/qmrebind - 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
Format
View formats within this collection
- 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
- 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
Primary associated publication
Software
- License
-
Creative Commons Attribution 4.0 International Public License
- Rights Holder
- UC Regents
- Copyright
-
Under copyright (US)
Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.
Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.
- Digital Object Made Available By
-
Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)
- Last Modified
2023-11-28