CCL: binding site/active site of new homolgous

 Sent to CCL by: "uzma  mahmood" [mehmoodchemist|*|gmail.com]
 Hi,
   I am computatiuonal chemist and i am working under the topic of Structural
 studies for this purpose firstly i select the homology modling to understand the
 insight of molecule but after built of homologs  i`m facing some problem
 regarding active site/binding site how can i evaluate that.......if any one know
 about something please tell me
 Because to solve this matter i do many more for example i take tempeletPDB
 sturtures and extract their ligand, find the centroids and apply on my new
 homologus in term of docking sence but no significant interaction i found so i
 think may be it`s centriods problem or either homologs problem this site is also
 overcome by using minmization technique...........
 can anybody help me....?
 Thanks