542192
doi
10.5281/zenodo.542192
oai:zenodo.org:542192
Niel Henriksen
University of California San Diego
Michael Gilson
University of California San Diego
Sample calculation using protein APR
Germano Heinzelmann
Universidade Federal de Santa Catarina
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
attach-pull-release method, BRD4 bromodomain, standard binding free energy, free energy methods, MBAR
<p>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. </p>
The results for this calculation, and for other ligands and water models, are to be published soon.
Zenodo
2017-04-11
info:eu-repo/semantics/other
795828
1579893953.913757
1687893
md5:4423d3860e96a95567c99dc8b7537d6a
https://zenodo.org/records/542192/files/scripts.tar.gz
5492521627
md5:ade8d730ca1653e19ccbe5dd1a8aecad
https://zenodo.org/records/542192/files/sample-calculation.tar.gz
public
isVersionOf
doi