Co-crystallizing; examining the interaction between truncated protein preparations and drug using Surface Plasmon Resonance Technology
Go for site map (site prediction) function in Schrodinger software for finding out the drug binding site to the target. Also in some other software you can go for random docking that will give you a rough estimation of all the proteins that can be altered by the drug.
Hope it might help you...
I agree with Panhaj but unfortunately the modeling without the actual coordinates does not give you reliable results and more often than not the predictions can not be confirmed when anotomic structure is resolved.
The PubChem homepage can help us to do this!
The link is: http://pubchem.ncbi.nlm.nih.gov/
Kind regards,
Arlan.
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