Hi
I have tried docking a unit cell of a nanoparticle onto protein (rigid blind docking) using autodock. Is it reasonable enough to assume the docked site (only one site was observed with low energy and 100% population with 2A cutoff) to be the desired protein-nanoparticle interaction site? or the nanoparticle must be of proper dimensions?
Also, is autodock an appropriate tool for such calculations (even if proper sizes are taken into account)?