From owner-chemistry[ AT ]ccl.net Mon Mar 23 14:51:01 2009
From: "Sebastian Radestock sebastian|a|radestock.net" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: [Fwd: CCL: RNA DOCKING]
Message-Id: <-38910-090323115129-14436-EsNfr6an51/cN72tvjlIVA .. server.ccl.net>
X-Original-From: Sebastian Radestock <sebastian::radestock.net>
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Date: Mon, 23 Mar 2009 16:51:13 +0100
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Sent to CCL by: Sebastian Radestock [sebastian{=}radestock.net]
Dear Elvis,

> 2.Can I get some score function directing toward RNA system(free of charg=
e
> and convenient) to rescore my docking poses and pick out correct poses
> from different docking poses?
>
> 3.Does anyone have any suggestion to RNA docking? How can I do precise
> docking to RNAs system?

For docking ligands to RNA molecules you might use DrugScore_RNA.
DrugScore_RNA is a knowledge-based scoring function. DrugScore has
been used as a function for re-scoring receptor-ligand complexes, and
it has been adapted to be used as an energy function in docking with
AutoDock.

Here are some references of interest:
* Pfeffer, P., Gohlke, H. DrugScore_RNA - Knowledge-based scoring
function to predict RNA-ligand interactions. J. Chem. Inf. Model.
2007, 47, 1868-1876.
* Radestock, S., Boehm, M., Gohlke, H. Improving Binding Mode
Predictions by Docking into Protein-Specifically Adapted Potential
Fields. J. Med. Chem. 2005, 48, 5466 - 5479.
* Sotriffer, C. A., Gohlke, H., Klebe, G. Docking into knowledge-based
potential fields: A comparative evaluation of DrugScore. J. Med. Chem.
2002, 45, 1967-1970.

Kind regards,
Sebastian.


--=20
Sebastian Radestock, Dipl.-Bioinformatiker
Computational Pharmaceutical Chemistry
Christian-Albrechts-Universit=E4t zu Kiel
URL: http://www.radestock.net
Mail: sebastian]|[radestock.net