The use of a genetic algorithm search for molecular mechanics (MM3)-based conformational analysis of oligosaccharides.
Journal article, 2005

We have implemented a system called glygal that can perform conformational searches on oligosaccharides using several different genetic algorithm (GA) search methods. The searches are performed in the torsion angle conformational space, considering both the primary glycosidic linkages as well as the pendant groups (C-5–C-6 and hydroxyl groups) where energy calculations are performed using the MM3(96) force field. The system includes a graphical user interface for setting calculation parameters and incorporates a 3D molecular viewer. The system was tested using dozens of structures and we present two case studies for two previously investigated O-specific oligosaccharides of the Shigella dysenteriae type 2 and 4. The results obtained using glygal show a significant reduction in the number of structures that need to be sampled in order to find the best conformation, as compared to filtered systematic search.

molecular mechanics sugar conformation genetic algorithm

Author

Per-Georg Nyholm

University of Gothenburg

Avi Nahmany

University of Gothenburg

F. Strino

University of Gothenburg

Graham Kemp

Chalmers, Computer Science and Engineering (Chalmers), Computing Science (Chalmers)

Per-Georg Nyholm

University of Gothenburg

Carbohydrate Research

0008-6215 (ISSN)

Vol. 340 5 1059-1064

Subject Categories

Other Basic Medicine

DOI

10.1016/j.carres.2004.12.037

More information

Created

10/7/2017