Atomic-level models, nucleic acid structures

This paper describes the development and initial applications of nab, a computer language for modeling biological macromolecules. It was developed to create atomic-level models of nucleic acid structures such as stem-loops, pseudoknots, multi-armed junctions and catalytic RNAs, and to investigate biological processes that involve nucleic acids, such as hybridization, branch migration at junctions, and DNA replication. 

Of the three major components of biological structure, the proteins, nucleic acids, and polysaccharides, least is known about the polysaccharides at the secondary and tertiary level of molecular structure. This is because the polysaccharides cannot be obtained in crystals which are large enough for single crystal X-ray or neutron structure analysis. What structural information there is comes from fiber X-ray diffraction patterns. However good these diffraction patterns are, the structures derived from them will always be model-dependent. This is because the number of variable atomic parameters which determine the diffraction intensities exceeds the number of observed intensities. 

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