Work on nucleic acid structure has continued in a variety of collaborations and directions. The RNA structure analysis system has expanded to include more functionality for analyzing RNA conformations from various perspectives. This has involved the development of new algorithms to explore secondary and tertiary structural motifs. This has made available an experimental computer workbench to allow a researcher to interactively pursue various areas of interest concerning RNA structure in a coherent way. This includes both the use of facilities to explore in detail multiple structures as well as individual RNA structures. This system permits queries of relationships that exist in the RNA secondary and tertiary structure problem domain involving various software/hardware complexes available at the FCRDC and elsewhere. A large portion of the system has been ported to a SUN thus allowing broader access. Algorithms have been developed that involve RNA secondary and tertiary structure analysis specifically the measurement and visualization of structural similarity from global and contextual viewpoints. A fast algorithm has been developed to compare RNA structures using the concept of levels of abstraction. This permits the definition and searching of structures from loose to a more restricted specifications. The system has been used to study the fine structural details of the HIV-1 rev responsive element (RRE), termination structures of lambda TR2 and is currently being used to study the termination structure of the 5' non-coding regions of poliovirus and the relationships between RNA secondary and tertiary structures. Exploratory work has continued utilizing an scanning tunneling microscope to visualize the fine structure of molecules, specifically RNA.
