I have been attempting to dock some fatty acid ligands to an equilibrated
fatty acid outer membrane transport protein macromolecule. The original PDB
from rcsb includes binded FAs showing the binding sites of the original
protein, and I would like to show the similarity/differences of these
binding sites on a close relative of the rcsb PDB protein.
I have been successful as far as running the process and attaining results,
but each minutely different structure pulled from different frames of the
equilibration dcd results in different docking clusters. I am using a
larger grid size (80x80x120) to map the inner protein binding sites as well
as the outer binding sites. Sometimes the clusters are tightly packed and
other times they are extremely spread out. I am leaving the settings at the
default, and run 1 docking simulation for ten FAs, extracting the resulting
10 PDBs from each docking.
I was wondering how to make the dockings more consistent, either by
changing the docking settings or by choosing better equilibrated
structures. I don't want to cherry pick data, so I would like to have some
rationality behind why chose one equilibrated structure over another. I am
really excited about this, but I am worried about forcing results. I
haven't found any papers of anyone using this type of method as of yet, so
I am hoping someone on this forum has some advice on the issue.