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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