An algorithm for converting a virtual-bond chain into a complete polypeptide backbone chain.
A systematic analysis is presented of the algorithm for converting a virtual-bond chain, defined by the coordinates of the alpha-carbons of a given protein, into a complete polypeptide backbone.  An alternative algorithm, based upon the same set of geometric parameters used in the Purisima-Scheraga algorithm but with a different "linkage map" of the algorithmic procedures, is proposed.  The global virtual-bond chain geometric constraints are more easily separable from the loal peptide geometric and energetic constraints derived from, for example, the Ramachandran criterion, within the framework of this approach.
Luo
N
N
Department of Biophysics, Roswell Park Memorial Institute, Buffalo, NY 14263, USA.
Shibata
M
M
Rein
R
R
D000465:Algorithms; D002625:Chemistry, Organic; D008433:Mathematics; D008958:Models, Molecular; D055601:Organic Chemistry Phenomena; D010455:Peptides / Q000032:analysis / Q000737:chemistry*; D011487:Protein Conformation
D010455:Peptides