The development of model fitting and completion program for automated iterative nucleic acid refinement

Over the past decade, many nucleic acid structures have been determined, which have contributed to our understanding of their biological functions. However, the crystals containing nucleic acid often poorly diffract X-rays. This makes electron density interpretation difficult and requires a great deal of expertise in crystallography and knowledge of nucleic acid structure. Here, new programs called NAFIT and NABUILD for fitting and extending nucleic acid models are presented. These programs can be used as modules for the automated refinement system, LAFIRE, as well as acting as independent programs. NAFIT performs sequential grouped fitting with empirical torsion angle restraints and anti-bumping restraints including hydrogen atoms. NABUILD extends the model using a skeletonized map in a coarse-grained manner. It was shown that NAFIT greatly improved electron density fit and geometric quality and NABUILD with iterative refinement significantly reduced Rfree factor.

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