BrickworX is a computer program that builds crystal structure models using recurrent RNA motifs or B-DNA double helices.
The program requires a MTZ file with structure factor amplitudes and phases. The program is able to predict the phosphate atom positions with the help of a support vector machine classifier and can also accept the positions of the phosphorous atoms that are specified by the user. In the latter case, the program can read phosphorus atom positions from a user-defined file in PDB format. Since quality of the input phosphorus atom positions is crucial for the program success, the predicted pattern should be revised manually in difficult cases.
The user must also specify whether the target structure is RNA or DNA. This is required for determination of correct double helix geometry for building an initial model. Furthermore if a target molecule is RNA, Brickworx will additionally try to build non-helical recurrent motifs derived from the RNA Bricks database.
On output Brickworx provides two files in PDB format; the predicted phosphorus atom pattern (if applicable) and a model in a full-atom representation.
Authors and Contact
Brickworx was developed by Grzegorz Chojnowski, Tomasz Waleń, Paweł Piątkowski, Wojciech Potrzebowski, and Janusz M. Bujnicki Feel free to contact us at gchojnowski with any comments, suggestions or bug-reports.
ReferenceChojnowski G, Waleń T, Piątkowski P, Potrzebowski W and Bujnicki JM Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps
Acta Cryst. (2015). D71, 697-705. doi: 10.1107/S1399004715000383 [pdf]