Software

Shape: automatic conformation prediction of carbohydrates using a genetic algorithm

Jimmy Rosen¹ , Laurence Miguet² and Serge Pérez²

¹  Bio Organic Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands

²  Centre de Recherches sur les Macromolecules Vegetales, CNRS, BP 53, F-38041 Grenoble, France

author email corresponding author email

Journal of Cheminformatics 2009, 1:16doi:10.1186/1758-2946-1-16

Published:	21 September 2009

Abstract

Background

Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dimensional structure studies. Modelling procedures generally require significant training and computing resources, which is often impractical for most experimental chemists and biologists. Shape has been developed to improve the availability of modelling in this field.

Results

The Shape software package has been developed for simplicity of use and conformation prediction performance. A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling. Carbohydrates up to a few hundred atoms in size can be investigated on common computer hardware. It has been shown to perform well for the prediction of over four hundred bioactive oligosaccharides, as well as compare favourably with previously published studies on carbohydrate conformation prediction.

Conclusion

The Shape fully automated conformation prediction can be used by scientists who lack significant modelling training, and performs well on computing hardware such as laptops and desktops. It can also be deployed on computer clusters for increased capacity. The prediction accuracy under the default settings is good, as it agrees well with experimental data and previously published conformation prediction studies. This software is available both as open source and under commercial licenses.