title: The use of a genetic algorithm search for molecular mechanics (MM3)-based conformational analysis of oligosaccharides.
abstract: 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.
authors.affiliation: Department of Medical Biochemistry, Göteborg University, Medicinaregatan 7B, Box 440, SE-405 30 Göteborg, Sweden.
authors.forename: Abraham
authors.initials: A
authors.lastname: Nahmany
authors.forename: Francesco
authors.initials: F
authors.lastname: Strino
authors.forename: Jimmy
authors.initials: J
authors.lastname: Rosen
authors.forename: Graham J L
authors.initials: GJ
authors.lastname: Kemp
authors.forename: Per-Georg
authors.initials: PG
authors.lastname: Nyholm
mesh_terms: D000465:Algorithms; D002236:Carbohydrate Conformation; D019081:O Antigens / Q000737:chemistry; D009844:Oligosaccharides / Q000737:chemistry*; D012762:Shigella dysenteriae / Q000737:chemistry; D012984:Software
chemical_list: D019081:O Antigens; D009844:Oligosaccharides