CCL: [Fwd: CCL: RNA DOCKING]



 Sent to CCL by: Sebastian Radestock [sebastian{=}radestock.net]
 Dear Elvis,
 > 2.Can I get some score function directing toward RNA system(free of charge
 > 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.
 --
 Sebastian Radestock, Dipl.-Bioinformatiker
 Computational Pharmaceutical Chemistry
 Christian-Albrechts-Universität zu Kiel
 URL: http://www.radestock.net
 Mail: sebastian]|[radestock.net