Remote access to Sweet-II

3D structure models via url/uri

The Sweet-II tool can be used to create 3D structure models of carbohydrate chains.

This service is also available to external sites. If you provide a glycoinformatics database and would like to give your users access to 3D structure information, you simply need to establish a link to the following url:

http://www.glycosciences.de/tools/sweet-remote/get3dmodel.php?linucs={add your structure in LINUCS notation here}

The information on the glycan structure to be modeled is passed to the tool via the linucs paramter.
[This parameter requires the structure in (url-encoded) LINUCS notation; see below for further notation options]

For example, a model of the Sialyl-LewisX structure can be accessed by the following link:

http://www.glycosciences.de/tools/sweet-remote/get3dmodel.php?linucs=[][b-D-GlcpNAc]{[(3%2b1)][a-L-Fucp]{}[(4%2b1)][b-D-Galp]{[(3%2b2)][a-D-Neup5Ac]{}}}

The N-glycan core with (1-3)-linked core fucose is retrieved by this link:

http://www.glycosciences.de/tools/sweet-remote/get3dmodel.php?linucs=[][b-D-GlcpNAc]{[(3%2b1)][a-L-Fucp]{}[(4%2b1)][b-D-GlcpNAc]{[(4%2b1)][b-D-Manp]{[(3%2b1)][a-D-Manp]{}[(6%2b1)][a-D-Manp]{}}}}


Options

If you want to get access to the 3D structure file in PDB format, you can add a parameter &outformat=pdb to the url.

Furthermore, you can select to retrieve a Tinker-optimized structure by adding a parameter &optimize=true to the url.




Access by alternative notation formats:

Notation options

In addition to LINUCS, the structure can be encoded in CSDB format, LinearCode, CarbBank format, or GlycoCT format.

In that case you need to set the paramters structure and format. The former passes the glycan structure to the tool, and the latter indicates the notation format of the structure [csdb | linearcode | carbbank | glycoct_condensed | glycoct_xml].

For example, Sialyl-LewisX model introduced above can be retrieved in CSDB notation as follows:

http://www.glycosciences.de/tools/sweet-remote/get3dmodel.php?format=csdb&structure=Ac(1-5)aXNeup(2-3)bDGalp(1-4)[aLFucp(1-3),Ac(1-2)]bDGlcpN

or using LinearCode notation via:

http://www.glycosciences.de/tools/sweet-remote/get3dmodel.php?format=linearcode&NNa3Ab4(Fa3)GNb

Note:
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