UCT CS Research Document Archive

CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation.

Kuttel, Michelle, Yue Mao, Magnus Lundberg and Goran Widmalm (2011) CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation.. In Proceedings 7th IEEE International Conference on e-Science, Stockholm, Sweden.

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Abstract

CarbBuilder is a software tool for building 3D structures of carbohydrates, which are the most structurally varied of all molecular classes. CarbBuilder was designed with the dual aims of portability and adaptability, using an iterative software development approach. CarbBuilder employs a simple algorithm, using heuristics based upon experimental data to con- vert a primary structure description of a carbohydrate molecule into a three-dimensional structure file. This straightforward approach means that CarbBuilder can be easily adapted: users can add additional monosaccharide building blocks or alter the conformational defaults to suit specific requirements. The output carbohydrate structure can be used for subsequent molecular simulation investigations. CarbBuilder is freely available and portable: it is a text-based stand-alone program that can run on Windows, Linux and MacOS X systems without installation.

EPrint Type:Conference Paper
Subjects:D Software: D.2 SOFTWARE ENGINEERING
J Computer Applications: J.2 PHYSICAL SCIENCES AND ENGINEERING
I Computing Methodologies: I.6 SIMULATION AND MODELING
ID Code:704
Deposited By:Kuttel, Michelle
Deposited On:06 October 2011