Data from: Prediction of Threonine-Tyrosine Kinase Receptor-Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics
Data from: Prediction of Threonine-Tyrosine Kinase Receptor-Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics
About this collection
- Extent
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1 digital object.
- Cite This Work
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Votapka, Lane W.; Ojha, Anupam A.; Naoya, Asada; Amaro, Rommie E. (2024). Data from: Prediction of Threonine-Tyrosine Kinase Receptor-Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0571C7G
- Description
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This collection contains a set of full Simulation Enable Estimation of Kinetic Rates (SEEKR) simulations and calculation results for eight inhibitors of the threonine tyrosine kinase (TTK) target. For each of these systems, starting structures were generated with metadynamics and steered molecular dynamics for generating starting structures in order to compare the two methods. Full simulation files as well as milestoning analysis results are included, as well as convergence outputs and plots.
- Creation Date
- 2022-05 to 2024-06
- Date Issued
- 2024
- Principal Investigator
- Researchers
- Funding
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This research was performed with the support of the Merkin Fellowship from the University of California San Diego. All simulations were performed using the Popeye computing cluster at the San Diego Supercomputing Center (SDSC) and the Delta supercomputing system at the National Center for Supercomputing Applications (NCSA), University of Illinois Urbana-Champaign. The authors acknowledge support from NSF Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS) CHE060063.
- Topics
Format
View formats within this collection
- Language
- English
- Identifier
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Identifier: Anupam A. 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
- Votapka, Lane W., Ojha, Anupam A., Asada, Naoya, Amaro, Rommie E., Prediction of Threonine-Tyrosine Kinase Receptor-Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics (in prep).
- AmberTools (ambermd.org)
- Browndye (browndye.ucsd.edu)
- OpenMM (openmm.org)
- SEEKR: https://github.com/seekrcentral/seekr2
- Image credit: Lane W. Votapka. "TTK in complex with BAY 1217389."
Primary associated publication
Software
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