Ojha, Anupam A.; Srivastava, Ambuj; Votapka, Lane W.; Amaro, Rommie E. (2022). Data from: Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations. UC San Diego Library Digital Collections. https://doi.org/10.6075/J01Z44MN

The data set contains all the files necessary to recreate the results in the paper "Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations." The data contains the Simulation Enabled Estimation of Kinetic Rates (SEEKR) simulations for the JAK2 and JAK3-ligand complexes with instructions to compute the residence times of the ligands in these complexes.

• 2020 to 2022

• 2022

• Amaro, Rommie E.
• Ojha, Anupam A.

• Srivastava, Ambuj
• Votapka, Lane W.

The SEEKR2 program should be downloaded from https://github.com/seekrcentral/seekr2 and https://github.com/seekrcentral/seekr2_openmm_plugin.

Corresponding author: Rommie Amaro

A.A.O. acknowledges the support of the Molecular Sciences Software Institute (MolSSI) fellowship under NSF grant OAC-1547580. R.E.A. acknowledges support from NSF Extreme Science and Engineering Discovery Environment (XSEDE) CHE060063 and NIH GM132826. All simulations were performed using the Triton Shared Computing Cluster (TSCC) and Expanse at the San Diego Supercomputing Center (SDSC). The latter allocation is supported by NSF XSEDE CHE060063 to R.E.A.

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

• data

• English

Identifier: Ambuj Srivastava: https://orcid.org/0000-0003-1023-6124

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

Primary associated publication

• Anupam Anand Ojha, Ambuj Srivastava, Lane William Votapka, and Rommie E. Amaro. Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. Journal of Chemical Information and Modeling 2023 63 (8), 2469-2482. https://doi.org/10.1021/acs.jcim.2c01589
• Ojha, A.A., Srivastava, A., Votapka, L.W. and Amaro, R.E., 2022. Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations. bioRxiv. https://www.biorxiv.org/content/10.1101/2022.11.10.516058v3.abstract

Software

• SEEKR2 OpenMM Plugin GitHub repository: https://github.com/seekrcentral/seekr2
• Simulation-Enabled Estimation of Kinetic Rates - Version 2 GitHub repository: https://github.com/seekrcentral/seekr2_openmm_plugin

Creative Commons Attribution 4.0 International Public License

• UC Regents

Under copyright (US)

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Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)

2023-08-01