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

Michelle A. Sahai, Sándor Lovas, Gregory A. Chass, Botond Penke, Imre G. Csizmadia

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)169-218
Number of pages50
JournalJournal of Molecular Structure: THEOCHEM
Volume666-667
DOIs
Publication statusPublished - Dec 29 2003

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Keywords

  • Ab initio
  • Atomic numbering
  • Internal coordinates
  • Oligopeptide
  • Peptide computations
  • Peptide folding
  • Protein folding

ASJC Scopus subject areas

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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