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

Per-Georg Nyholm ; Avi Nahmany ; Francesco Strino ; Graham J.L. Kemp (Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers)) ; Jimmy Rosen
Carbohydrate Research (0008-6215). Vol. 340 (2005), 5, p. 1059-1064.
[Artikel, refereegranskad vetenskaplig]

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.

Nyckelord: molecular mechanics sugar conformation genetic algorithm

Denna post skapades 2010-02-28. Senast ändrad 2012-08-20.
CPL Pubid: 116521


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Institutioner (Chalmers)

Institutionen för medicinsk och fysiologisk kemi (1991-2005)
Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers)



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