Find or compare structures
Use SugarDB to search bacterial carbohydrate primary structures and inspect automatically generated glycan diagrams.
Research software
Tools for bacterial carbohydrate research
SugarDB and CarbBuilder help researchers move from carbohydrate primary structures to searchable knowledge and simulation-ready three-dimensional molecular models.
Why these tools?
Making complex carbohydrate structures easier to use
Bacterial carbohydrates are structurally diverse, highly branched and difficult to represent using tools designed primarily for proteins or small molecules. This software programme addresses two linked needs: finding and comparing curated carbohydrate structures, and rapidly generating reliable starting models for molecular simulation.
The tools arise directly from research in computational glycochemistry and are designed around the specialised workflows of carbohydrate scientists.
Web platform
SugarDB
SugarDB is a user-centred repository for bacterial carbohydrate primary structures. It was developed to make specialised structural data faster to search, easier to interpret and simpler to extend.
- Carbohydrate-specific queries for rapid structure searches
- Immediate visual overviews of database contents
- Automatic Symbol Nomenclature for Glycans diagrams from CASPER text
- Fast addition of newly characterised structures
- A design that can be extended to additional pathogens and datasets
Desktop modelling tool
CarbBuilder
CarbBuilder generates three-dimensional molecular structures of complex oligo- and polysaccharides from textual primary-structure specifications. It supports structures ranging from monosaccharides to large, branched polysaccharides and provides practical starting models for molecular simulation.
The application was developed in C# for the .NET framework. It runs on Windows and can also be used on macOS and Linux through Mono.
Latest release: CarbBuilder 2.1.48
Approximately 4.1 MB
If you use CarbBuilder, please cite:
M. M. Kuttel, J. Ståhle and G. Widmalm. “CarbBuilder: Software for Building Molecular Models of Complex Oligo- and Polysaccharide Structures.” Journal of Computational Chemistry 37(22), 2098–2105 (2016). doi:10.1002/jcc.24428.
M. Kuttel, Y. Mao, G. Widmalm and M. Lundborg. “CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation.” IEEE e-Science (2011), 395–402. Read the paper.
Where to begin
Choose the tool for your task
Build a molecular model
Use CarbBuilder when you have a primary-structure specification and need an initial three-dimensional carbohydrate model.