Name
Title | ||
|---|---|---|
Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3 |
Abstract | ||
|---|---|---|
The potential energy hypersurfaces (PES) of several carbohydrate molecules were studied with a new algorithm for conformational searches, CICADA (Channels in Conformational Space Analyzed by Driver Approach) interfaced with the molecular mechanics program MM3(92). The method requires (1) one or a few low-energy conformations as starting points; and (2) designation of the torsion angles important for understanding the conformational behavior of the molecule. The PES is explored by driving separately each selected torsion angle (in both directions) with a concomitant full-geometry optimization at each increment (except for the driven angle). When a minimum has been detected, the molecule is freely optimized, and the minima so detected are then stored if not encountered previously. The new minima serve as starting structures for further explorations. The results from CICADA permit prediction of relative and absolute flexibility and conformational softness for both the entire molecule as well as for individual group rotations and local minima. The carbohydrates analyzed were Me-alpha-D-glucopyranoside, beta-D-GlcNAc(1-2)alpha-D-Man, and alpha-D-GalNAc(1-3)[alpha-L-Fuc(1-2)]Gal-O-Me. All the low-energy conformers along with the transition states and flexibilities features were characterized. CICADA found all minima and low-energy conversion pathways for the disaccharide that were found by a traditional grid search. In contrast to the grid search method, CICADA concentrates mostly on the exploration of the low-energy regions of the PES, thereby saving a significant amount of computational time. The performance of the method opens new routes for exploring conformational space of larger molecules, such as oligosaccharides. (C) 1995 by John Wiley & Sons, Inc. |
Year | DOI | Venue |
|---|---|---|
1995 | 10.1002/jcc.540160305 | JOURNAL OF COMPUTATIONAL CHEMISTRY |
Field | DocType | Volume |
Conformational isomerism,Torsion (mechanics),Molecule,Computational chemistry,Chemistry,Maxima and minima,Transition state,Potential energy,Dihedral angle | Journal | 16 |
Issue | ISSN | Citations |
3 | 0192-8651 | 2 |
PageRank | References | Authors |
0.48 | 1 | 3 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Jaroslav Koca | 1 | 193 | 25.16 |
| Serge Pérez | 2 | 5 | 1.57 |
| Anne Imberty | 3 | 3 | 1.50 |