Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment.

ABSTRACT: An algorithm is proposed for the conversion of a virtual-bond polypeptide chain (connected C alpha atoms) to an all-atom backbone, based on determining the most extensive hydrogen-bond network between the peptide groups of the backbone, while maintaining all of the backbone atoms in energetically feasible conformations. Hydrogen bonding is represented by aligning the peptide-group dipoles. These peptide groups are not contiguous in the amino acid sequence. The first dipoles to be aligned are those that are both sufficiently close in space to be arranged in approximately linear arrays termed dipole paths. The criteria used in the construction of dipole paths are: to assure good alignment of the greatest possible number of dipoles that are close in space; to optimize the electrostatic intera

SUBMITTER: Liwo A 

PROVIDER: S-EPMC2142257 | biostudies-literature | 1993 Oct

REPOSITORIES: biostudies-literature