19] Computer modeling and display of RNA secondary and tertiary structures

Abstract

Publisher Summary This chapter presents a computer program, ribonucleic acid structure editor (RNASE), for the construction and representation of RNA secondary and tertiary structures.’ The program can be used to predict and display helical regions of RNA secondary structures. After selection of helices, a three-dimensional image of the molecule can be obtained. The RNASE program is an attempt to address certain weaknesses in other structural prediction programs and to extend display graphics into the relatively unexploited realm of tertiary structure. For helix generation and energy calculations, a simple folding algorithm generates a list of all possible helical regions. The structures generated in the previous section involve only nested base-paired regions. However, recent research has documented the importance of less orthodox structures in RNA molecules called pseudoknots. Most secondary structure prediction algorithms do not consider such conformations. Knot search and selection is done by starting with the list of all possible helices and the particular combination selected for the secondary structure from above. Then, a list of potential knots is made from the complex helix list by removing all helices which contain nucleotides common to helices selected for the secondary structure.