Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland)
A computer program that builds crystal structure models of nucleic acid molecules is presented. 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.
- OSTI ID:
- 22347697
- Journal Information:
- Acta Crystallographica. Section D: Biological Crystallography, Vol. 71, Issue Pt 3; Other Information: PMCID: PMC4356372; PMID: 25760616; PUBLISHER-ID: wa5082; OAI: oai:pubmedcentral.nih.gov:4356372; Copyright (c) Chojnowski et al. 2015; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
- Country of Publication:
- Denmark
- Language:
- English
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