ADL: Receptor questions for Autodock

Wenjing.Shi at Wenjing.Shi at
Fri Apr 17 07:31:39 PDT 2009


Thank you very much for your input to my question regarding ligand database.
Itƒs very helpful. Today, I would like to hear your comments on how to use
Autodock  for my project.

As I mentioned before, I'm searching small molecules that potentially bind to
MHC-peptid complex (e.g. MHC-CMV peptide). In my case, the receptor is the
MHC-peptide complex (i.e. MHC and peptide, two molecules), while the ligands
are the small molecules. After reading related materials, I found that all the
docking was done with ligands and one macromolecule (e.g. protein). So my
question is that whether I can use Autodock for my study. How should I prepare
my receptor---MHC-peptide complex?

Also, I'm wondering whether there is any chance of short-term training (e.g.
one week or shorter) for the Autodock program? If, there is, please give me
more information.

Thank you again.



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