Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps
Authors:
- Grzegorz Chojnowski,
- Tomasz Waleń,
- Paweł Pia¸tkowski,
- Wojciech Potrzebowski,
- Janusz Marek 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.
- Record ID
- UAM89917d94bb8c462687be568bea8271f2
- Author
- Journal series
- Acta Crystallographica Section D-Biological Crystallography, ISSN 0907-4449
- Issue year
- 2015
- Vol
- 71
- Pages
- 697-705
- ASJC Classification
- ;
- DOI
- DOI:10.1107/S1399004715000383 Opening in a new tab
- Language
- (en) English
- Score (nominal)
- 45
- Score source
- journalList
- Score
- Publication indicators
- = 1; = 4; : 2013 (2 years) = 7.232 - 2013 (5 years) =9.416
- Uniform Resource Identifier
- https://researchportal.amu.edu.pl/info/article/UAM89917d94bb8c462687be568bea8271f2/
- URN
urn:amu-prod:UAM89917d94bb8c462687be568bea8271f2
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or PerishOpening in a new tab system.