Molecular views of damaged DNA: Adaptation of the Program DUPLEX to parallel architectures

Conference · Thu Sep 01 00:00:00 EDT 1994

OSTI ID:10179306

Hingerty, B E; Crawford, O H ^[1]; Broyde, S ^[2]; Wagner, R A ^[3]

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1. Oak Ridge National Lab., TN (United States)
2. New York Univ., NY (United States). Biology Dept.
3. Duke Univ., Durham, NC (United States). Dept. of Computer Science

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. The first stage of adaptation to parallel computers is described.

• Research Organization: Oak Ridge National Lab., TN (United States); New York Univ., NY (United States)
• Sponsoring Organization: USDOE, Washington, DC (United States); National Insts. of Health, Bethesda, MD (United States)
• DOE Contract Number: AC05-84OR21400; FG02-90ER60931
• OSTI ID: 10179306
• Report Number(s): CONF-9407126-1; ON: DE94018118; CNN: Grant CA28038; Grant RR06458; TRN: 94:009236
• Resource Relation: Conference: 2. DOE-Energy Research Power users symposium,Rockville, MD (United States),12 Jul 1994; Other Information: PBD: [1994]
• Country of Publication: United States
• Language: English

Related Subjects

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTANT EFFECTS ON LIVING ORGS. AND BIOL. MAT.
59 BASIC BIOLOGICAL SCIENCES
COMPUTERS
PARALLEL PROCESSING
BENZOPYRENE
CARCINOGENESIS
DNA ADDUCTS
MOLECULAR STRUCTURE
NUCLEIC ACIDS
POLYCYCLIC AROMATIC HYDROCARBONS
NUCLEOTIDES
560300
550200
CHEMICALS METABOLISM AND TOXICOLOGY
BIOCHEMISTRY