Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

Acta Crystallographica. Section D, Biological Crystallography
Grzegorz ChojnowskiJanusz M Bujnicki

Abstract

Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

References

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Citations

Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Grzegorz ChojnowskiVictor S Lamzin
Aug 3, 2019·Acta Crystallographica. Section D, Structural Biology·Grzegorz ChojnowskiVictor S Lamzin

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