ADL: How to add distance constraints to Autodock?

tony at tony at
Wed Oct 31 11:00:11 PDT 2007

Dear All,

I'm trying to dock a chemically modified peptide inhibitor (165 atoms) to
the active site of an enzyme. The exact location of the binding site is
known. In addition, due to a common mode of binding observed in other
structurally unrelated inhibitors, I can anticipate not only the relative
position of the enzyme and the inhibitor but also the possible
interactions between both molecules. Thus, a set of atoms of my inhibitor
should to positioned within a certain distance to a set of atoms of the
enzyme molecule so that they can form hydrogen bonds.

I've performed several runs using Autodock 4.0 with a grid centered in the
binding site but none of the resulting docked conformations satisfied the
above criteria.

Is there any way to apply distance constraints in Autodock 4.0?
Simething like: Consider only conformations where atom A from the ligand is
within distance B from the atom C in the receptor molecule.

Alternatively, could you suggest me any other approach to perform flexible
docking of two molecules using user defined distance constraints.

Any help will be highly appreciated.

Thank you in advance.


PS.A rigid body docking is not helpful since at least the ligand has to
undergo a conformational change.

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