Jupyter Notebook and associated modules and data set for performing Markov state model and conformational analyses of apo-HIV-1 protease from molecular dynamics simulations

MOLECULAR DYNAMICS MARKOV STATE MODEL AND CONFORMATIONAL GATING FACTOR ANALYSIS FOR HIV-1 PROTEASE

Author: Dr. S. Kashif Sadiq Affiliation: 1. Heidelberg Institute for Theoretical Studies, HITS gGmbH 2. European Moelcular Biology Laboratory Correspondence: [email protected]

Last modified: 18.06.2021

Manuscript: S. Kashif Sadiq, Abraham Muñiz Chicharro, Patrick Friedrich, Rebecca Wade, A multiscale approach for computing gated ligand binding from molecular dynamics and Brownian dynamics simulations. (2021)

A preprint of the manuscript is available at: https://doi.org/10.1101/2021.06.22.449380

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Please read README.txt in the data/MD/ directory for further instructions on working with this data set and associated analyis scripts

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