Torsion space nucleic acids molecular mechanics program DUPLEX: Surveying conformation space by potential energy minimization. Progress report

摘要

The molecular mechanics program DUPLE-X has proven useful in surveying the conformation space of unmodified DNAs and RNAs, and covalently damaged DNAs, by potential energy minimization. The reduced variable set of torsion angle space, together with search strategies that flat explore small subunits, permit location of low energy structures from high energy positions. Prediction of structure in the absence of data, though difficult is possible with large numbers of trials. With NMR data to guide the searches in first stage trials, generation of final unrestrained low energy forms that are within bounds of the data is achieved with fewer trials.