Thanks everyone for the tips. Actually, I need this information to improve my
analysis on drug/protein interaction.
Best regards:)
Gerardo A. Libreros
Universidade de São Paulo
Laboratório de Biologia Estrutural Aplicada
Sent from my iPhone
> On 7 Jun 2017, at 18:34, Jared Sampson
Easiest way is to line up molecule pairs or chain pairs in COOT and see if
there are equivalent waters.
If the number of waters is too large to inspect manually,
save the superposed structures to disk, grep out the waters from each into a
separate files,
and use a program like
How about
WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct
structure-based drug design?
Ben
On 7 Jun 2017, at 07:59, Eleanor Dodson wrote:
Many years ago I wrote code to label waters with a code related to the
residue/atom they were
Many years ago I wrote code to label waters with a code related to the
residue/atom they were Hbonded to , so then you could check whether all OH
TYR 227 in each chain had an associated water.. But it used non-standard
water naming ..
Easiest way is to line up molecule pairs or chain pairs in
Hi everyone, does anyone know any strategy or program (besides pywater) to
identify conserved waters in a protein?
Thanks,
Gerardo
Dear all,
and especially all of you involved in the development of refinement
programs,
in low resolution refinement we always include structural information we
actually do not see in the electron density (side chains, riding
hydrogens) since we know that these atoms are there. But what about
board [CCP4BB@JISCMAIL.AC.UK] de la part de Guenter Fritz
[guenter.fr...@uni-konstanz.de]
Date d'envoi : samedi 2 novembre 2013 16:04
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Conserved water positions in low resolution refinement?
Dear all,
and especially all of you involved in the development