Contact information

Authors

Magdalena Rother - implementation

Kristian Rother - architecture and unit tests

Tomasz Puton - model validation and testing

Juliusz Stasiewicz - identification and nomenclature of nucleotides

Andrzej Wojtowicz - CCD Loop Closer implementation

Janusz Bujnicki - concept and supervision

Technical Support:

lenam@amu.edu.pl

Laboratory of Structural Bioinformatics
Collegium Biologicum
Institute of Molecular Biology and Biotechnology
Adam Mickiewicz University
ul. Umultowska 89
61-614 Poznan, Poland

Head of the Laboratory: Janusz M. Bujnicki, PhD, DSc.:

Email: iamb@genesilico.pl
Office: (+48-61) 829-58-39

Citing

When using ModeRNA, please cite:

ModeRNA: a tool for comparative modeling of RNA 3D structure. Rother M, Rother K, Puton T, Bujnicki JM. Nucleic Acids Res. 2011 Feb 7. [Epub ahead of print]

Acknowledgements

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.
Special thanks go to the group of Russ Altman, who provided us with their modeling example to test ModeRNA.

References

Components of ModeRNA are based upon the following pieces of scientific literature:

[1] 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.

[2] 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.

[3] Gendron P, Lemieux S, Major F. Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol. 2001 May 18;308(5):919-36.

[4] 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.

[5] 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.