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. 2014 Sep 23;1(Pt 6):387-92.
doi: 10.1107/S2052252514019290. eCollection 2014 Nov 1.

Automated nucleic acid chain tracing in real time

Kevin Cowtan  1
Affiliations

Automated nucleic acid chain tracing in real time

Kevin Cowtan. IUCrJ. .

Abstract

The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the 'fingerprint' of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into the Coot software package.

Keywords: Coot; nucleic acid chain tracing.

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Figures

Figure 1
Figure 1
High and low probe points (spheres and crosses, respectively) for (a) the sugar target and (b) the phosphate target. The average electron density over the reference set of nucleotides is shown.
Figure 2
Figure 2
Comparison of the value of the search target score as a function of translational coordinate error for the correctly oriented sugar and phosphate targets, using either the s minmax or s mean scoring functions. The shading represents a density histogram of counts, with light shading for 1–4 or dark shading for 5+ counts per bin. Dashed lines show the regression of score on distance for distances less than 2.5 Å.
Figure 3
Figure 3
Comparison of autobuilt nucleotides with the final structure for 3cw5 at 3.1 Å resolution. The backbone trace of the full structure is show using a worm representation, and backbone atoms for the autobuilt model are shown as bonds.
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