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Application of the distance geometry algorithm to cyclic oligopeptide conformation searches

✍ Scribed by Catherine E. Peishoff; J. Scott Dixon; Kenneth D. Kopple

Publisher
Wiley (John Wiley & Sons)
Year
1990
Tongue
English
Weight
870 KB
Volume
30
Category
Article
ISSN
0006-3525

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✦ Synopsis

The distance geometry algorithm as embodied in the program DGEOM was examined as a method for searching cyclic peptide conformations. Conformations were randomly generated using covalent distance and chirality constraints, but torsion angle rather than distance sampling was used for 1,4 relationships. Structures so generated were energy minimized by a fixed number of iterations using the molecular mechanics program AMBER 3.0; electrostatic terms were excluded in the minimization. The effectiveness of this procedure in sampling conformational space for cyclic peptides was measured by the ability to recover, from a set of 500 structures, conformations similar to those experimentally observed for six cyclic peptides containing from 8 to 20 rotatable backbone bonds. Structures similar to experimental structures were recovered in a 16-bond case, but not for a 20-bond example. The method was also applied, with constraints on the peptide bond angles w , to an additional example containing 21 ring bonds.

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