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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. 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. Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp) 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
Type
dataset
Identifier
ark:/20775/bb9125378m
Language
English
Subject
Milestoning Molecular dynamics Simulation Enabled Estimation of Kinetic Rates (SEEKR) Markovian milestoning with Voronoi tessellations Chemical sciences Brownian dynamics Quantum mechanics Theoretical and computational chemistry
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