[Dock-fans] virtual screening using dock?

venkat vkabas at yahoo.com
Wed Jun 24 12:53:57 PDT 2009


I am trying to find the small molecule that could interfere with protein - protein interface. I am new to docking and have few questions in mind before
I start ,

I know for the protein without complex can be used for docking as whole.

For protein - protein interactions, I do have to keep both complex as receptor molecule and search for small molecule that binds near the interface?That did not make sense cause small molecule is not going to interfere with the already filled interface with other protein.

I think I could use two pdbs separtely and trying to find the small molecule to the known interface region?

any help could be appreciate



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