Votapka, Lane W.; Stokely, Andrew M.; Ojha, Anupam A.; Amaro, Rommie E. (2022). Data from: SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0668DDR

This data set contains the files necessary to recreate the results in the paper "SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine". Specifically, the data for the host-guest, trypsin-benzamidine, and jak2-ligand6 systems are contained here, with instructions for how to compute kinetics and thermodynamics quantities, as well as convergence and plots.

• 2020-08 to 2022-03

• 2022

• Amaro, Rommie E.
• Ojha, Anupam A.
• Stokely, Andrew M.
• Votapka, Lane W.

All data were generated using SEEKR2 v2.5.1-beta, which is also required to analyze and visualize the data in this collection.

Software modules and versions:
SEEKR2 v2.5.1-beta
Python 3.8
Numpy 1.22.3
Scipy 1.7.3
matplotlib 3.5.2

This work was funded in part by the National Science Foundation through XSEDE supercomputing resources provided via TG-CHE060073 to R.E.A. A.A.O. acknowledges support from the Molecular Sciences Software Institute (MolSSI) fellowship under NSF grant OAC-1547580.

• Brownian dynamics
• Computational biophysics
• Computational chemistry
• Host-guest
• Janus kinase
• Kinetics
• Molecular dynamics
• Rate constant
• Simulation-Enabled Estimation of Kinetic Rates version 2 (SEEKR2)
• Statistical mechanics
• Theoretical chemistry
• Thermodynamics
• Trypsin

• data

• English

Identifier: Andrew M. Stokely: https://orcid.org/0000-0002-3750-5323

Identifier: Anupam A. Ojha: https://orcid.org/0000-0001-6588-3092

Identifier: Lane W. Votapka: http://orcid.org/0000-0002-0865-5867

Identifier: Rommie E. Amaro: https://orcid.org/0000-0002-9275-9553

Primary associated publication

• Lane W. Votapka, Andrew M. Stokely, Anupam A. Ojha, and Rommie E. Amaro (2022). SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. Journal of Chemical Information and Modeling 62 (13), 3253-3262. https://doi.org/10.1021/acs.jcim.2c00501

Creative Commons Attribution 4.0 International Public License

• UC Regents

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2023-08-04