CarbBuilder: An Adjustable Tool for Building 3D Molecular Structures of Carbohydrates for Molecular Simulation

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 convert 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.