Building up conformers from these starting blocks can quickly generate a very large tree of structures. The key to MC-SYM's success is its ability to prune this tree, and the user has considerable flexibility in designing this pruning process. Sets of low energy dinucleotide conformers were created by selecting one value from each of the sterically allowed ranges for the six backbone torsion angles and x. Instead of an exhaustive build- up search over a small set of conformers, this method samples a much larger region of conformational space by randomly combining members of a larger set of initial conformers. Unlike strict build-up procedures, any member of the initial set is allowed to follow any other member, even if their corresponding torsion angles do not exactly match, a concession to the extreme flexibility of the nucleic acid backbone. A key feature determined the probabilities of the initial conformers so that the probability of each created structure accurately reflected its energy.
Special procedures allow base-pairs to be preserved during deformations.
This procedure allows simple algorithmic descriptions to be constructed for non-regular structures like intercalation sites, hairpins, pseudoknots and bent helices. Rigid-body transformations often provide a good way to place the bases. Work along these lines suggests that the relationship is complicated and non-linear. The sequence is decomposed into 3'-nucleotide monophosphates. Each nucleotide has as independent variables its six helicoidal parameters, its glycosidic torsion angle, three sugar angles, two sugar torsions and two backbone torsions.