title: RCrane: semi-automated RNA model building.
abstract: RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
authors.forename: Kevin S
authors.initials: KS
authors.lastname: Keating
authors.forename: Anna Marie
authors.initials: AM
authors.lastname: Pyle
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D001331:Automation; D001671:Biochemistry / Q000379:methods; D019295:Computational Biology / Q000379:methods; D018360:Crystallography, X-Ray / Q000379:methods; D004583:Electrons; D046911:Macromolecular Substances / Q000737:chemistry*; D008968:Molecular Conformation; D009113:Muramidase / Q000737:chemistry; D009711:Nucleotides / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D046911:Macromolecular Substances; D009711:Nucleotides; D011506:Proteins; D012313:RNA; D009113:Muramidase