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: [log in to unmask]
>> Subject: Re: [ccp4bb] Straw poll: polysaccharide building?
>> To: [log in to unmask]
>>
>> 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:[log in to unmask]] On Behalf Of
>>> Kim Henrick
>>> Sent: Tuesday, July 26, 2011 11:44 AM
>>> To: [log in to unmask]
>>> 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
|