[phenixbb] Ligand conformations.

Katherine Sippel katherine.sippel at gmail.com
Wed Apr 6 09:49:54 PDT 2011

I would direct you to a conversation on the ccp4bb last year (
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;eb55b86e.1003 ). Don't
ask me how I remember this but what you are looking for specifically is
found in this reply by Artem Evdokimov.

"It's called cross-soaking and it is a fairly popular technique
especially in the industrial community where we sometimes have to work
with hundreds of ligands.

I've done it on several occasions and mostly have been pretty happy
with the results. Having said this I also would like to point out that
soaking is not always the same as co-crystallization in terms of the
ligand-protein interactions. An extreme case is shown in the paper
below (figure 5):


PDBID: 2i4g, 2i4h



Hope this helps,


On Wed, Apr 6, 2011 at 11:21 AM, Yuri <yuri.pompeu at ufl.edu> wrote:

> Has anyone ever reported seeing 2 different binding confromations for a
> ligand that was soaked vs. the same ligand co-crystallized?
> --
> Yuri Pompeu
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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
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