ADL: Pro-pro docking

Sharath Roy royshari87 at yahoo.in
Mon Apr 27 03:18:56 PDT 2009


HI
I have read some information about protein protein docking using AD4 in mailing list......

I have a modelled prot. of 356 a.a which has to be docked to a receptor complex......I know where the modelled prot has to bind.........
But what should i treat this new protein that i have to dock.......shall i treat it as a ligand and prepare its pdbqt co-ords or treat it as a rigid body again........

i read that we have to increase npts etc.....but what shud i treat the docking protein as .....and moreover if i knw the loop/residues of the modelled prot, then can i specify these so that it allows the protein to move around the receptor.......

I am confused (sort of)......kindly suggest



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