The molecular mechanics program DUPLEX: Computing structures of carcinogen modified DNA by surveying the potential energy surface |
| |
Authors: | Brian E. Hingerty Suse Broyde |
| |
Affiliation: | (1) Health Sciences Research Division, Oak Ridge National Laboratory, 37831 Oak Ridge, TN, USA;(2) Biology Department, New York University, 10003 New York, NY, USA |
| |
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. |
| |
Keywords: | Molecular mechanics DNA carcinogens structures potential energy surface |
本文献已被 SpringerLink 等数据库收录! |
|