CCL: protein-small molecules reactions

[Gonçalo C. Justino <jgcj- -fct.unl.pt>]

 dear all,

i'm studying the reaction between a protein and a small
 molecule. from experiments we know it forms covalent adducts to four residues,
 which have been clearly identified.

my question is: how can i predict,
 from the structures of both the protein and the molecule, which are the residues
 most likely to react?
 
i was planning to get a solvent accessibility map of the protein and then
 "react" the molecule to those residues (we know it's an sn2
 reaction), but i can't figure out what approach to use to model those
 reactions using the **whole protein**.
 
any comments will be very much
 appreciated!

cheers,
g.



-- 
Gonçalo
 Justino,
 Ph.D.
----------------------------------------------------
[Computational
 & Radical BioChemistry]
 Requimte/CQFB - Department of Chemistry
Faculty of Sciences and
 Technology
New University of Lisbon
2829-516
 Caparica
Portugal
Phone: (+351) 212 948 300 ext. 10971
Fax: (+351) 212
 948 550
----------------------------------------------------
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