A modular numbering system of selected oligopeptides for molecular computations: using pre-computed amino acid building blocks

A standardized numbering system has been developed to define the relative spatial orientation of all constituent atomic nuclei in model peptide systems. The system is expected to improve efficiency in the formulation of initial structural estimates and analysis of the results emerging from molecular orbital computations on oligopeptides, catalogued in a database. This standard provides each peptide residue with a numeric definition of its own, enabling the numerical differentiation of individual residues in a peptide chain; without the use of visualization tools. The standardized method was used in effective geometry optimizations of selected conformers of selected peptides. Such an arrangement facilitates automation of data generation and proper database management of oligo and polypeptides. The extension from single residues to a variety of oligopeptides is elaborated upon.