[Dock-fans] discrepancy between rigid and flex

Francesco Pietra chiendarret at gmail.com
Mon May 4 02:30:01 PDT 2009

I wonder whether a large discrepancy between the docking region
between rigid and flex dock is a sign of some artifact in setting up
the procedures. This implies that i have carefully tried to discover
artifacts at no avail. For example, with same input files, changing
from allHIP state to allHIS state of the protein (and removing the
extra  proton of HIS from the pdb file) leads from a normal situation
(i.e., rigid and flex differing mainly  in the ligand conformation) to
an absurd situation of rigid and flex poses being located nearly as
far apart as the range of the protein could allow, while the
conformational difference is the same as from the allHIP state of the

I understand that without showing the files one can't expect much from
such a question, however, i am asking about general experience
suggesting what may be grossly wrong under the described observations.

If one asks what is likely to be the HIS/HIE/HIP state of the protein
i can only answer that the complexity is such that pKa-solving
programs got confused, proving of no help.

francesco pietra

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