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1.  Geometric properties of nucleic acids with potential for autobuilding 
Algorithms and geometrical properties are described for the automated building of nucleic acids in experimental electron density.
Medium- to high-resolution X-ray structures of DNA and RNA molecules were investigated to find geometric properties useful for automated model building in crystallographic electron-density maps. We describe a simple method, starting from a list of electron-density ‘blobs’, for identifying backbone phosphates and nucleic acid bases based on properties of the local electron-density distribution. This knowledge should be useful for the automated building of nucleic acid models into electron-density maps. We show that the distances and angles involving C1′ and the P atoms, using the pseudo-torsion angles and that describe the …P—C1′—P—C1′… chain, provide a promising basis for building the nucleic acid polymer. These quantities show reasonably narrow distributions with asymmetry that should allow the direction of the phosphate backbone to be established.
PMCID: PMC3006036  PMID: 21173468
nucleic acids; autobuilding; geometric properties; electron-density distribution

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