The molecular mechanics program DUPLEX: Computing structures of carcinogen modified DNA by surveying the potential energy surface

Brian E. Hingerty, Suse Broyde

Research output: Contribution to journalArticlepeer-review

Abstract

The nucleic acids molecular mechanics program DUPLEX has been designed with useful features for surveying the potential energy surface of polynucleotides, especially ones that are modified by polycyclic aromatic carcinogens. The program features helpful strategies for addressing the multiple minimum problem: (1) the reduced variable domain of torsion angle space; (2) search strategies that emphasize large scale searches for smaller subunits, followed by building to larger units by a variety of strategies; (3) the use of penalty functions to aid the minimizer in locating selected structural types in first stage minimizations; penalty functions are released in terminal minimizations to yield final unrestrained minimum energy conformations. Predictive capability is illustrated by DNA modified by activated benzo[a]pyrenes.

Original languageEnglish (US)
Pages (from-to)219-227
Number of pages9
JournalMolecular Engineering
Volume5
Issue number1-3
DOIs
StatePublished - Mar 1995

Keywords

  • DNA
  • Molecular mechanics
  • carcinogens
  • potential energy surface
  • structures

ASJC Scopus subject areas

  • Biochemistry

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