Algorithms for automated building of nucleic acid structures

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", to identify backbone phosphates and bases based on properties of the local electron density distribution.We have used this knowledge to propose an algorithm for the automated building of nucleic acid models into electron density maps.The algorithm is based on distances and angles involving C1' and the phosphorus atoms and involves the pseudo-torsion angles η' and θ' that describe the ..P-C1'-P-C1'.. chain.These quantities show reasonably narrow distributions and an asymmetry that allows the direction of the phosphate backbone to be established.