skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

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.

Authors:
 [1];  [1];  [2]; ;  [1];  [1];  [2]
  1. International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland)
  2. (Poland)
Publication Date:
OSTI Identifier:
22347697
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 71; Journal 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)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; COMPUTER CODES; CRYSTAL STRUCTURE; CRYSTALS; DENSITY; DNA; ELECTRON DENSITY; ELECTRONS; MOLECULES; PEAKS; PHOSPHATES; RESOLUTION

Citation Formats

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl, Waleń, Tomasz, University of Warsaw, Banacha 2, 02-097 Warsaw, Piątkowski, Paweł, Potrzebowski, Wojciech, Bujnicki, Janusz M., and Adam Mickiewicz University, Umultowska 89, 61-614 Poznan. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps. Denmark: N. p., 2015. Web. doi:10.1107/S1399004715000383.
Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl, Waleń, Tomasz, University of Warsaw, Banacha 2, 02-097 Warsaw, Piątkowski, Paweł, Potrzebowski, Wojciech, Bujnicki, Janusz M., & Adam Mickiewicz University, Umultowska 89, 61-614 Poznan. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps. Denmark. doi:10.1107/S1399004715000383.
Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl, Waleń, Tomasz, University of Warsaw, Banacha 2, 02-097 Warsaw, Piątkowski, Paweł, Potrzebowski, Wojciech, Bujnicki, Janusz M., and Adam Mickiewicz University, Umultowska 89, 61-614 Poznan. Sun . "Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps". Denmark. doi:10.1107/S1399004715000383.
@article{osti_22347697,
title = {Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps},
author = {Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl and Waleń, Tomasz and University of Warsaw, Banacha 2, 02-097 Warsaw and Piątkowski, Paweł and Potrzebowski, Wojciech and Bujnicki, Janusz M. and Adam Mickiewicz University, Umultowska 89, 61-614 Poznan},
abstractNote = {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.},
doi = {10.1107/S1399004715000383},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = Pt 3,
volume = 71,
place = {Denmark},
year = {Sun Mar 01 00:00:00 EST 2015},
month = {Sun Mar 01 00:00:00 EST 2015}
}