Sample Calculation Using Protein Apr

Sample calculation using the protein attach-pull-release (APR) method on the BZT-7 ligand to the BRD4 first bromodomain, with the SPC/E water model. Instructions for the automatic creation of the system are included in the automated.bash script in the ./Base-SPC/ folder, and the ./BZT-7-SPC/ folder contains the sample calculation. To obtain the binding free energies from the simulations using MBAR, instructions can be found in the ./Base-SPC/analysis/get-results.bash script.

The results for this calculation, and for other ligands and water models, are to be published soon.

Related Organizations

Universidade Federal de Santa Catarina
Brazil
University of California, San Diego
United States

Keywords

attach-pull-release method, BRD4 bromodomain, standard binding free energy, free energy methods, MBAR

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