Nucleic Acids Research Advance Access originally published online on October 14, 2008
Nucleic Acids Research 2009 37(Database issue):D118-D121; doi:10.1093/nar/gkn710
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, Database issue D118-D121
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
MODOMICS: a database of RNA modification pathways. 2008 update
1Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland, 2Max Planck Institute for Developmental Biology, Department 1, Protein Evolution Spemannstr. 35, 72076 Tuebingen, Germany, 3Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, PL-02-190 Warsaw, Poland, 4Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and 5IGM, Univ Paris-Sud, UMR 8621, Orsay, F 91405, France
*To whom correspondence should be addressed. Tel: +48-22 597 0752; Fax: +48 22 597 0715; Email: krother{at}genesilico.pl
Correspondence may also be addressed to Henri Grosjean. Tel: +33(0)1-6915 4637; Fax: +33(0)1-6915 4629; Email: henri.grosjean{at}igmots.u-psud.fr; Janusz M. Bujnicki. Tel: +48-22 597 0750; Fax: +48 22 597 0715; Email: iamb{at}genesilico.pl
Received September 15, 2008. Accepted September 29, 2008.
MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected to substantial improvements. It provides comprehensive information on the chemical structure of modified nucleosides, pathways of their biosynthesis, sequences of RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also provides cross-references to other databases and to literature. In addition to the previously available manually curated tRNA sequences from a few model organisms, we have now included additional tRNAs and rRNAs, and all RNAs with 3D structures in the Nucleic Acid Database, in which modified nucleosides are present. In total, 3460 modified bases in RNA sequences of different organisms have been annotated. New RNA-modifying enzymes have been also added. The current collection of enzymes includes mainly proteins for the model organisms Escherichia coli and Saccharomyces cerevisiae, and is currently being expanded to include proteins from other organisms, in particular Archaea and Homo sapiens. For enzymes with known structures, links are provided to the corresponding Protein Data Bank entries, while for many others homology models have been created. Many new options for database searching and querying have been included. MODOMICS can be accessed at http://genesilico.pl/modomics.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Umitsu, H. Nishimasu, A. Noma, T. Suzuki, R. Ishitani, and O. Nureki Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2 PNAS, September 15, 2009; 106(37): 15616 - 15621. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Taoka, Y. Yamauchi, Y. Nobe, S. Masaki, H. Nakayama, H. Ishikawa, N. Takahashi, and T. Isobe An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes Nucleic Acids Res., September 9, 2009; (2009) gkp732v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ye, R. Jia, J. Lin, M. Ju, J. Peng, A. Xu, and L. Zhang Structural organization of box C/D RNA-guided RNA methyltransferase PNAS, August 18, 2009; 106(33): 13808 - 13813. [Abstract] [Full Text] [PDF]
|
|