Laboratory of Structural Bioinformatics
Head of the Laboratory: Janusz M. Bujnicki, PhD, DSc.:
When using ModeRNA, please cite:
Credit goes to our lab colleagues Ewa Wywial, Pawel Skiba, Piotr
Byzia, Irina Tuszynska, Joanna Kasprzak, Jurek Orlowski, Pawel Lukasz, Tomasz Osinski, Marcin Domagalski, Anna Czerwoniec, Stanislaw Dunin-Horkavicz, Marcin Skorupski, and Marcin Feder for their comments and constructive criticism during development. The PDB parser of Moderna has been extracted from BioPython with kind support of Thomas Hamelryck. The unit test framework was brought near to us by Sandra Smit, Rob Knight, and Gavin Huttley. We also would like to thank Neocles Leontis, Fabrice Jossinet, Francois Major, and Eric Westhof who provided helpful advice on various occasions.
Components of ModeRNA are based upon the following pieces of scientific literature:
 Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K. MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res. 2008 Oct 14.
 Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 2003 Jul 1;31(13):3450-60.
 Gendron P, Lemieux S, Major F. Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol. 2001 May 18;308(5):919-36.
 Michalsky E, Goede A, Preissner R. Loops In Proteins (LIP)–a comprehensive loop database for homology modelling. Protein Eng. 2003 Dec;16(12):979-85.
 Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 1;25(11):1422-3. Epub 2009 Mar 20.