Data from: Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations
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Description | Instructions for recreating the results from the data set. |
JAK data
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Description | The data set contains the SEEKR2 simulation files for the JAK2 and JAK3-ligand complexes. |
- Collection
- Cite This Work
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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
- Description
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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.
- Creation Date
- 2020 to 2022
- Date Issued
- 2022
- Authors
- Contributors
- Technical Details
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The SEEKR2 program should be downloaded from https://github.com/seekrcentral/seekr2 and https://github.com/seekrcentral/seekr2_openmm_plugin.
- Note
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Corresponding author: Rommie Amaro
- Funding
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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.
- Topics
Format
View formats within this collection
- Language
- English
- Identifier
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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
- Related Resources
- 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
- 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
Primary associated publication
Software
- License
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Creative Commons Attribution 4.0 International Public License
- Rights Holder
- UC Regents
- Copyright
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Under copyright (US)
Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.
Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.
- Digital Object Made Available By
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Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)
- Last Modified
2023-08-01