ADL: AutoDock 4 and protein-protein docking

Gianluca Interlandi gianluca at
Tue Oct 9 12:35:39 PDT 2007

Dear list,

I'm new to autodock.

I would like to dock two globular proteins of ca. 200 amino acids each. 
The structure of the two unbound proteins is known but not the structure 
of the complex. I need to perform a global search blind docking (i.e., no 
knowledge of the bound state). The backbone can be rigid but the side 
chains at the interface should be flexible.

Is autodock 4 appropriate for this kind of problem? The autodock main page 
says: "It enables AutoDock's use in evaluating protein-protein 
interactions." What does that mean? Can I use autodock for protein-protein 

Any help would be very appreciated,


Dr. Gianluca Interlandi gianluca at
                    +1 (206) 685 4435
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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