[Dock-fans] convert pdb to flexibase format

Yi Shang mirandaisbest at gmail.com
Tue Dec 23 10:21:39 PST 2014


Hi There,
I found the crystal ligand has really bad docking score in my DOCK3.6
screen (top 75% in 4 million compounds). The docked pose has one rotatable
bond (C-CH2-OH) orientated unfavorably, which might cause the bad score.

Now I am wondering if I can re-generate the flexibase file from crystal
ligand coordinates, to make sure the active orientation is included, and
then redo docking.

I was following http://wiki.bkslab.org/index.php/Flexibase_Format, I don't
understand why for some compounds the downloaded database from ZINC have
more than 1 Family lines (for a single compound).

Thank you for your help!


-- 
Yi  Shang,   Ph.D.
postdoctoral research associate
Icahn School of Medicine at Mount Sinai
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