computational expenses and to slowing down the performance
substantially.- These values ofkandttMDwere calibrated for GAGs of length
up to heptasaccharide [14]. An increase of k and a decrease of
ttMDcould lead to the insufficient conformational sampling of
the ligand during the targeted MD step. On the contrary, a
decrease ofkand an elongation of the targeted MD step would
lead to the scenario when many ligands are not properly tar-
geted to the receptor but would be uniformly distributed on
the sphere defined by a distance restraint, which would lead to
the need of many more repetitions of the procedure to obtain a
statistical ensemble of docking solutions suitable for further
analysis. These values ofkandttMDfor significantly longer
ligands, however, should be calibrated in terms of translational
and rotational freedom by comparing their RMSD in an MD
simulation with the RMSD expected from the targeting
through the shortest possible path. - In order to substantially decrease the invested computational
time, it is practically convenient to remove all waters and
counterions from the structure of the obtained complex, to
add them again and to use the equilibration protocol described
in Subheading2.2 (steps 5and 6 ) before the free MD step. In
this case the minimum distance from solute atoms to the box
boundaries could be increased to 8–9 A ̊ to avoid possible
artifacts related to the insufficient treatment of system’s
hydration. - Some runs can end up with the ligand in an unbound state after
the tMD step or the ligand can unbind during the free MD
step. Depending on how many events like this are observed,
100 repeated procedures could be enough or not. We recom-
mend obtaining at least 80–90 bound docking poses for the
further analysis. In case of longer GAG ligands this number can
be increased to obtain higher statistical significance of the
results.
Acknowledgments
This work was supported by National Science Center of Poland
(Narodowy Centrum Nauki, grant UMO-2016/21/P/ST4/
03995). This project received funding from the European Union’s
Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie grant agreement No. 665778.Solvent Inclusion in Docking Glycosaminoglycans 453