ADL: Pro-pro docking

home at home at
Tue Apr 28 01:18:46 PDT 2009

On Mon, 27 Apr 2009 15:48:56 +0530 (IST), Sharath Roy <royshari87 at>
> 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
> 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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sorry this is direct 2u, but I'm away .  The smaller prtn is ligand,
remember to correct /debump, charges/ of both structs.

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