Subject: modeling inhibitor in groove

From: Pedro Antonio Reche <reche:at:research.dfci.harvard.edu>
Date: Sat, 19 Jul 2003 11:27:58 -0400

Hi, I have a PDB of a kinase in complex with a inhibitor, and I would  
like to replace that inhibitor with a related compound. I have already  
generated a PDB file for this  compound but I do not  I have to  
proceed, and thereby any input about the software (better if unix open  
source), and strategy to replace the original inhibitor with this  
related compound will be greatly appreciated. Also, does anyone know of  
a software to overlay  3D structures of small molecules? I am thinking  
that overlaying the derivative compound with the inhibitor in the 3D  
structure of the kinase would be a possibility, but what software to  
use?!
Anyway,  any idea, or suggestion about best way to solve this problem  
will be greatly appreciated.
Cheers
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Pedro A Reche, PhD
MIF Bioinformatics Group Head
Dana-Farber Cancer Institute  (D1510A)                                   
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Harvard Medical School                                                   
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                             EM: reche:at:research.dfci.harvard.edu
Boston, MA 02115, USA                                                    
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