title: Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps.
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.
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Chojnowski
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Waleń
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Paweł
authors.initials: P
authors.lastname: Piątkowski
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Wojciech
authors.initials: W
authors.lastname: Potrzebowski
authors.affiliation: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012984:Software
chemical_list: D012313:RNA; D004247:DNA
keywords: Brickworx; model building; nucleic acids