[modeller_usage] Modelling of one conformation, docking another being a problem?

[Nataraj Balkrishnan <natarajmtech AT yahoo.co.uk>]

Dear modellers,
           I have modelled protein(Transmembrane protein) from a template,whose conformation avilable in closed state. But from litterature study I have inferred that my ligand able to interact with my model only at open conformation. Now my questions are,

1) wheather can I  proceed to docking with this model(modelled for closed conformation) to test the ligand interaction with the model?
2)Does docking softwares populary used, such as one I am having the Autodock will take care of this drawback?

Kidly help me,
B.Natara,
M.Tech.,(Bioinformatics),
SASTRA Deemed University,
Thanjavur,
Tamil Nadu,
India.

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