I want to model some complex polysaccharides containing non-conventional saccharides as building units. The structures should retain the proper glyscosidic linkage. Please suggest me some tools for the same.
I studied college chemistry over almost thirty years ago. So I am not familiar with specialized tools to serve this purpose. or if there are any of these tools that are open source. If not, I have worked with Autodesk Inventor and SolidWorks and both applications allow for adaptive parametric solid modeling, and geometric dimensioning and tolerancing. If all you need is a 3d model created with Euclidean geometry, these software applications should do the trick.
Did you search online? Over 250 molecular modeling software are available. Some of them are very good and can handle polysaccharide. Unless you are very specific, this modeling of your's seems routine!
Dear Dr. Khan,
Thanks for the kind facts. I am well aware of most of the software listed online and for your kind surprise have tried most of them. I do realise the importance of this portal and certainly the time of other people.
I am here because the sugars I am using as building unit are not the common ones and as being in this filed I know the importance of correctness of 3D structure of a small molecule.
Trying tio help you.
A wide collection of optimized structure of monosaccharide is freely available on the site glycopedia.eu (look for the resources section) whereas some basic notion of monosaccharide nomenclature is presented in one of the e-chapter of the site.
The glyco3D site (hosted at CERMAV) gives access to a Polysaccharide builder (associated with a scientifc article piblished recently).
In case of problem, please contact me, I would be happy to help.
Regards
Thank you Mr. Martin and Mr. Serge for the valuable suggestion of yours and the help you have offered.
I have used CarbBuilder (as suggested by Mr. Martin), SWEETII, chemsketch and glyco3D (as suggested by Mr. Serge). Though all these software have wide range of sugar units and are really good for routine polysaccharides but they are lacking in acidic sugars. And the polysaccharide I am trying to build contains acidic sugars.
I welcome any suggestion regarding the modeling of polysaccharides using acidic sugar as building units.
Once again thank you very much for your time.
I think that defining additional sugar units in CarbBuilder should be possible so the most straightforward action would be to contact the authors of the program . . .
Mr. Serge, I am trying to build a series of polysaccharides by incorporating MurNAc with different natural disaccharides and oligosaccharides.
Thank you Mr. Martin for the valuable suggestion. I will definitely contact the authors of CarbBuilder. Even myself have thought the same and have been trying to incorporate the monosaccharide in their file list.
I don't know if it has the glycans you need but this tool
http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1
has worked very nicely for my students.
Good luck
Daniel
Thank you all for your valuable time and discussions.
Special thanks to Mr. Martin for very useful suggestion and CarbBuilder (https://people.cs.uct.ac.za/~mkuttel/CBresidues.html) team members specially Prof. M. Kuttel and Prof. Goran Widmalm for their valuable help.
CarbBuilder really proved very useful to me with a very good and immediate support from Prof. Kuttel and team. I was able to design all the required structures for my work. The software really have a very good library of sugars.
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