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Application of the distance geometry algorithm to cyclic oligopeptide conformation searches
Author(s) -
Peishoff Catherine E.,
Dixon J. Scott,
Kopple Kenneth D.
Publication year - 1990
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360300107
Subject(s) - energy minimization , chemistry , molecular geometry , torsion (gastropod) , covalent bond , bond length , ring (chemistry) , algorithm , peptide bond , cyclic peptide , geometry , chirality (physics) , dihedral angle , crystallography , molecule , peptide , computational chemistry , mathematics , physics , medicine , biochemistry , nambu–jona lasinio model , surgery , organic chemistry , chiral symmetry breaking , quantum mechanics , hydrogen bond , crystal structure , quark
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 ω, to an additional example containing 21 ring bonds.