Host-guest binding remains
a major challenge in modern computational modelling. The newest 7<sup>th</sup>
statistical assessment of the modeling of proteins and ligands (SAMPL)
challenge contains a new series of host-guest systems. The TrimerTrip host
binds to 16 structurally diverse guests. Previously, we have successfully employed
the spherical coordinates as the collective variables coupled with the enhanced
sampling technique metadynamics to enhance the sampling of the
binding/unbinding event, search for possible binding poses and predict the
binding affinities in all three host-guest binding cases of the 6<sup>th</sup>
SAMPL challenge. In this work, we employed the same protocol to investigate the
TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the
SAMPL7 host, our simulations initiate from randomly selected configurations and
are proceeded long enough to obtain converged free energy estimates and search
for possible binding poses. The predicted binding affinities are in good agreement
with the experimental reference, and the obtained binding poses serve as a nice
starting point for end-point or alchemical free energy calculations.
SAMPL7 TrimerTrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations
