References

Please, cite the following paper in any published work which has made use of RNAComposer:

  • Popenda, M., Szachniuk, M., Antczak, M., Purzycka, K.J., Lukasiak, P., Bartol, N., Blazewicz, J., Adamiak, R.W. Automated 3D structure composition for large RNAs, Nucleic Acids Research, 2012, 40(14):e112 (doi:10.1093/nar/gks339).


The following papers can be also cited:

  • Purzycka, K.J., Popenda, M., Szachniuk, M., Antczak, M., Lukasiak, P., Blazewicz, J., Adamiak R.W. Automated 3D RNA structure prediction using the RNAComposer method for riboswitches, Methods in Enzymology: Computational Methods for Understanding Riboswitches, 2014, 553:3-34 (doi:10.1016/bs.mie.2014.10.050).
  • Antczak, M., Popenda, M., Zok, T., Sarzynska, J., Ratajczak, T., Tomczyk, K., Adamiak, R.W., Szachniuk, M. New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure, Acta Biochimica Polonica, 2016, 63(4):737-744 (doi:10.18388/abp.2016_1329).
  • Biesiada, M., Purzycka, K.J., Szachniuk, M., Blazewicz, J., Adamiak, R.W. Automated RNA 3D structure prediction with RNAComposer, RNA Structure Determination: Methods and Protocols, 2016, 199-215 (doi:10.1007/978-1-4939-6433-8).


Our other papers referring to RNAComposer and its applications are:

  • Popenda, M., Bielecki, L., Adamiak, R.W. High-throughput method for the prediction of low-resolution, three-dimensional RNA structures, Nucleic Acids Symposium Series, 2006, 50:67-68 (pdf).
  • Popenda, M., Blazewicz, M., Szachniuk, M., Adamiak, R.W. RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Research, 2008, 36:D386-D391 (doi:10.1093/nar/gkm786).
  • Popenda, M., Szachniuk, M., Blazewicz, M., Wasik, S., Burke, E.K., Blazewicz, J., Adamiak, R.W. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics, 2010, 11:231 (doi:10.1186/1471-2105-11-231).
  • Rybarczyk, A., Szostak, N., Antczak, M., Zok, T., Popenda, M., Adamiak, R.W., Blazewicz, J., Szachniuk, M. New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics, 2015, 16:276 (doi:10.1186/s12859-015-0718-6).
  • Biesiada, M., Pachulska-Wieczorek, K., Adamiak, R.W., Purzycka, K.J. RNAComposer and RNA 3D structure prediction for nanotechnology, Methods, 2016, 16:30045-7 (doi:10.1016/j.ymeth.2016.03.0102016).