A smart polysaacharide autobuilder mindful of geometry and biology (no
non-biological sugars and linkages, please) and not based on what is
already deposited in the pdb might cause a significant decrease in ccp4
and phenixbb traffic. So I am for it!
Engin
On 7/26/11 4:28 AM, Robbie Joosten wrote:
Hi Kim and Kevin,
Even then you can have chirality inversions during real-space refinement, which
would destroy the SWEET input model from. There is no substitute for common
sense (and validation) here.
That said, Kevin, something to autobuild carbohydrates (given a sequence) would
be awesome. I'd use it a lot. Just don't make a WMD (weapon of model
destruction).
Cheers,
Robbie
----------------------------------------
Date: Tue, 26 Jul 2011 11:06:03 +0100
From: henr...@ebi.ac.uk
Subject: Re: [ccp4bb] Straw poll: polysaccharide building?
To: CCP4BB@JISCMAIL.AC.UK
Yes but it is easier to take the sweet model for the required sequence
and fit that to density rather than do it residue by residue
which will lead to glycan structures unknown to the source
kim
Dear Kim,
I asume that Kevin plans to build in electron density maps. As far as I
can see Sweet will produce a model unhindered by experimental data.
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Kim Henrick
Sent: Tuesday, July 26, 2011 11:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Straw poll: polysaccharide building?
why not use
http://glycosciences.de/modeling/sweet2/doc/index.php
which works perfectly
and would save the duplication of effort
cut& paste
#---
a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+
|
b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+
|
|
a-L-Fucp-(1-3)+
b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-6)+
|
|
a-L-Fucp-(1-3)+
a-D-Manp-(1-6)+
|
|
b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Ga
lp-(1-4)-b-D-GlcpNAc-(1-2)+
| a-L-Fucp-(1-6)+
|
|
b-D-Galp-(1-4)+
|
b-D-GlcpNAc-(1-4)-Asn
|
|
|
b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+
b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+
|
|
|
a-L-Fucp-(1-3)+
b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)+
|
|
|
|
a-L-Fucp-(1-3)+
b-D-GlcpNAc-(1-4)+
|
|
|
|
a-L-Fucp-(1-3)+
a-D-Manp-(1-3)+
|
a-D-Neup5Ac-(2-6)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Gl
cpNAc-(1-3)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-2)+
and click and your o/p is as attached
apart from the poor excuse for a pdb file it has the model with
glycosidic torsion angles as expected as in glycomapsdb
Straw poll:
Are you interested in software to autobuild polysaccarides?
Kevin
p.s. I expect I'll have to spend at least a year working on the
problem before before I spell polysaccharide consistently.
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
