We have developed a suite of software prototypes for representation, building and investigation of carbohydrate structures, listed below.
CarbBuilder
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CarbBuilder is software for building 3D molecular structures of carbohydrates. CarbBuilder enables researchers to build a complex 3D carbohydrate model from a textual primary structure specification. CarbBuilder supports building with a wide range of monosaccharide and other residues. This application was developed using C# under .Net framework. It can be run from Windows, and, using the mono framework, MacOS and Linux. LATEST version: Download CarbBuilder v2.1.47 (~4.1MB) How to install and run CarbBuilder. The residues currently supported by CarbBuilder for building polysaccharide structures are listed here. Previous versions: Download CarbBuilder v2.1.46 (~4.1MB) Download CarbBuilder v2.1.45 (~3.8MB) If you use CarbBuilder, please reference: CarbBuilder: Software for Building Molecular Models of Complex Oligo- and Polysaccharide Structures. M. M. Kuttel, Jonas Stahle, and Goran Widmalm, J. Comput. Chem., J. Comput. Chem., 37(22), 2098-2105 (2016), DOI: 10.1002/jcc.24428. CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation Michelle Kuttel, Yue Mao, Goran Widmalm and Magnus Lundborg Proceedings of 7th IEEE International Conference on e-Science , 5-8 December 2011, Stockholm, Sweden, pages: 395-402 pdf (406 KB)
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SugarDB is a a prototype repository for the primary structure of bacterial carbohydrates developed following user-centred design process. SugarDB has a carbohydrate-specific query system for rapid searches, an intuitive interface to provide an instant overview of the contents of the database and to facilitate data access, automatic generation of Symbol Nomenclature for Glycans primary structure graphs from CASPER text and the ability to rapidly add new structures. SugarDB adheres to standardised usability principles and evaluation heuristics, with novel features to support research into bacterial carbohydrates. The SugarDB prototype can be extended to cover a wide range of other pathogens - contact us to add your structures. |
