The use of a genetic algorithm search for molecular mechanics (MM3)-based conformational analysis of oligosaccharides.
Artikel i vetenskaplig tidskrift, 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

Författare

Per-Georg Nyholm

Göteborgs universitet

Avi Nahmany

Göteborgs universitet

F. Strino

Göteborgs universitet

Graham Kemp

Chalmers, Data- och informationsteknik, Datavetenskap

Per-Georg Nyholm

Göteborgs universitet

Carbohydrate Research

0008-6215 (ISSN)

Vol. 340 5 1059-1064

Ämneskategorier

Annan medicinsk grundvetenskap

DOI

10.1016/j.carres.2004.12.037

Mer information

Skapat

2017-10-07