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)?
We recently published our findings on the P-gp interaction with various nanoparticles (fullerenes and carbon nanotube) using different docking algorithms, such as gradient optimisation algorithm (ADVina), Lamarckian genetic algorithm (FastDock), and shape-based approach (PatchDock) to estimate the binding affinities between these structures. Please refer to our publication.
Article Multidrug resistance protein P-Gp interaction with nanoparti...
Which are the characterisctics of the function score or algorithms of optimization for docking studies of carbon nanotubes
You can also try our Blind Docking server:
http://bio-hpc.ucam.edu/aquiles/
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