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About this collection

Extent

1 digital object.

Cite This Work

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

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

• Amaro, Rommie E.

Researchers

• Naoya, Asada
• Ojha, Anupam A.
• Votapka, Lane W.

Funding

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

• Brownian dynamics
• Chemical sciences
• Markovian milestoning with Voronoi tessellations
• Milestoning
• Molecular dynamics
• Quantum mechanics
• Simulation Enabled Estimation of Kinetic Rates (SEEKR)
• Theoretical and computational chemistry

Format

View formats within this collection

• data

Language

• English

Identifier

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

Primary associated publication

• 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).

Software

• AmberTools (ambermd.org)
• Browndye (browndye.ucsd.edu)
• OpenMM (openmm.org)
• SEEKR: https://github.com/seekrcentral/seekr2

Collection image

• Image credit: Lane W. Votapka. "The two possible exit paths of compound 37 from HSP90."