ADL: protein-protein docking with many flexible regions

Maurice Ho bokcmho at
Thu May 1 20:03:44 PDT 2008

It's an issue of choosing more torsions for the ligand and the putative 
docking site on the target.  Both the peptide ligand (13 aa long) and 
the docking site have more than 32 rotatable bonds.  Since the potential 
interactions are largely unknown, I have no preference on choosing which 
32 bonds to do first.  Is it reasonable to divide the groups of 
rotatable bonds into several subgroups of 32 in maximum with certain 
degree of overlaps and then do multiple docking to obtain more possible 
interactions?  Then is there any way to put all those results together 
as a whole?  Through clustering of different conformations?

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