Michelle Kuttel

 

Software

We have developed a suite of software prototypes for representation, building and investigation of carbohydrate structures, listed below.

CarbBuilder

JCC cover image

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 v2.1.44 (~3.8MB)[Corrected bDFruf building.]

How to install and run CarbBuilder.

The residues currently supported by CarbBuilder for building polysaccharide structures are listed here.

Previous versions:

Download CarbBuilder v2.1.43 (~3.8MB)[Added aDAra and bDAra residues.]

Download CarbBuilder v2.1.42 (~3.8MB)[23 AUGUST 2021- more linkage defaults]

Download CarbBuilder v2.1.41 (~3.8MB)[23 JULY 2021- added additional linkage defaults]

Download CarbBuilder v2.1.40 (~3.8MB) [29 MARCH 2021- fixed incorrect isomer for glycerol-3-phosphate]

Download CarbBuilder v2.1.39 (~3.8MB)[4 MARCH 2021- minor bug fixes]

Download CarbBuilder v2.1.38 (~3.8MB)[5 November 2020 - minor bug fixes]

Download CarbBuilder v2.1.35 (~3.8MB)[19 August 2020 - minor bug fixes]

Download CarbBuilder v2.1.34 (~3.8MB) [5 April 2020 Bug fix for missing O for P substituent not in postion 1]

Download CarbBuilder v2.1.33 (~3.8MB) [29 March 2020 added aDHep residue, also -j val option for random gaussian "jiggle" about phi and psi about val degrees.]

Download CarbBuilder v2.1.31 (~3.8MB) [25 Jul 2019 3, and 4-bond dihedral specification added]

Download CarbBuilder v2.1.30 (~797KB) [18 Feb 2019 bug fixes for Gro1P and Gro3P]

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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)

 

Glycano

Glycano sample strucutre

Representation of Human Bllod A antigen

Human Blood A Antigen

Glycano is a web-application for creating graphical representations of polysaccharide sequences: the simple ‘nodes-and-edges’ molecular graphs typically used to convey the structure of complex, branched glycans in research publications. Glycano enables users to rapidly build, edit, annotate, load and export molecular graphs that represent the key features of polysaccharide structure. Glycano allows the user to toggle between two symbols sets for representing the monosaccharide ’nodes’: the widely adopted Essentials of Glycobiology symbol nomenclature and our new symbol set, which conveys residue connectivity information spatially and has broad coverage of bacterial sugar residues (ketones, linear alditols etc.). Glycano is designed to have an intuitive interface which minimises mouse-clicks for rapid structure building.

The website is implemented in Javascript, with all major browsers supported.

Last updated: June 2022