[Dock-fans] question about enrichment factors

Yunierkis Perez Castillo yunierkis at uclv.edu.cu
Mon May 28 08:52:18 PDT 2007

Hi all.

I have read the paper suggested by Jonh regarding enrichment factors.
I found it very interesting, and I have some questions regarding my own
I'm working with a protein for which exist 4 clases of known inhibitors.
Only one of these type of inhibitors have known binding mode and the
crystal structure of one inhibitor in complex with the protein is
publicly available. The active site of the protein is also reported to
be quite flexible.
I'm able to reproduce the crystallographic structure of the ligand with
a RMSD of about 1A, which is no sufficient to evaluate the quality of my
docking procedure. Using the same protocol I'm not able to find any
reliable binding pose for any of the rest three classes of inhibitors.
I'm now interested in the evaluation of the enrichment factor using my
docking procedure.
How much realistic will be the calculation of enrichment factors if I
know that i can't find any reliable binding mode (and hence scoring
values) for most of known ligands?
If I use only the class of inhibitors for which the binding mode is
known then the enrichment factor will not be a reliable measure of the
quality of my docking procedure. Is that right?
Thanks in advance for any help


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