Data from: Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations

Ojha, Anupam A.; Author; https://orcid.org/0000-0001-6588-3092; Srivastava, Ambuj; Contributor; https://orcid.org/0000-0003-1023-6124; Votapka, Lane W.; Contributor; https://orcid.org/0000-0002-0865-5867; Amaro, Rommie E.; Corresponding Author; https://orcid.org/0000-0002-9275-9553
0000-0003-1023-6124

The data set contains the files necessary to recreate the residence times of the ligands for the JAK2 and JAK3 complexes 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. 

Please cite as:
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

Corresponding author:
Rommie E. Amaro − University of California, San Diego, La
Jolla, California 92093, United States; orcid.org/0000-
0002-9275-9553; Email: ramaro@ucsd.edu

Primary associated publication:

Ojha, Anupam Anand, Ambuj Srivastava, Lane William Votapka, and Rommie E. Amaro. "Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations." bioRxiv (2022). https://www.biorxiv.org/content/10.1101/2022.11.10.516058v3.abstract

Instructions:

To compute the residence times of the ligands in JAK2
and JAK3 proteins, please follow the given steps:
1. Make sure the SEEKR2 program is installed by following the steps given on GitHub: 
(a) https://github.com/seekrcentral/seekr2
(b) https://github.com/seekrcentral/seekr2_openmm_plugin

2. Create a conda environment with the SEEKR2 environment and activate it.

3. Untar the downloaded JAK data and place it in any given directory. 

4. Go to the results folder and make the following changes in the get_residence_times.py file:
seekr2_pwd = "/home/aaojha/seekr2/seekr2" # PWD where the SEEKR2 program is installed, to be changed by the user
jak_pwd = "/home/aaojha/Downloads/jak_data" # PWD where the JAK data is downloaded, to be changed by the user

5. In the results folder, run the following scripts:
(a) python get_residence_times.py
(b) python plot_residence_times.py