protein domains involved in epigenetic regulation,
are able to bind small molecules with high affinity. In the present
study, we report free energy calculations for the binding of seven
ligands to the first BRD4 bromodomain, using the attach-pull-release
(APR) method to compute the reversible work of removing the ligands
from the binding site and then allowing the protein to relax conformationally.
We test three different water models, TIP3P, TIP4PEw, and SPC/E, as
well as the GAFF and GAFF2 para…
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