title: New model-fitting and model-completion programs for automated iterative nucleic acid refinement.
abstract: In the past decade many structures of nucleic acids have been determined, which have contributed to our understanding of their biological functions. However, crystals containing nucleic acids often diffract X-rays poorly. 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 in the automated refinement system LAFIRE, as well as acting as independent programs. NAFIT performs sequential grouped fitting with empirical torsion-angle restraints and antibumping restraints including H atoms. NABUILD extends the model using a skeletonized map in a coarse-grained manner. It has been shown that NAFIT greatly improves electron-density fit and geometric quality and that iterative refinement with NABUILD significantly reduces the Rfree factor.
authors.affiliation: Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.
authors.forename: Keitaro
authors.initials: K
authors.lastname: Yamashita
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhou
authors.forename: Isao
authors.initials: I
authors.lastname: Tanaka
authors.forename: Min
authors.initials: M
authors.lastname: Yao
mesh_terms: D018360:Crystallography, X-Ray / Q000379:methods*; D008958:Models, Molecular; D008968:Molecular Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D012984:Software
chemical_list: D009696:Nucleic Acids
keywords: LAFIRE; automatic refinement; nucleic acid model building; nucleic acid model fitting; real-space refinement