[Dock-fans] How to Dock peptide

John Irwin jir322 at gmail.com
Thu Feb 23 08:58:47 PST 2017


Possible, yes. Recommended, no.  DOCK 3.7 uses the rigid fragment +
decorations paradigm to sample conformations.  A peptide, even 3 residues
long, has too many internal degrees of freedom, and the "rigid fragment"
will likely be an aromatic side chain, if present, which may be peripheral.

For a case like this, I would recommend Rosetta.

Good docking





On Wed, Feb 22, 2017 at 11:36 PM, lina zhao <xinniwo at gmail.com> wrote:

> Hi
>
> I have a peptide, 7 residues Long.
>
> Whether is it possible to use dock3.6 to do the dock, mainly how to
> prepare the database.
>
> Thanks, Liv
>
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>
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