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PMID: 17947322 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

The 3D rRNA modification maps database: with interactive tools for ribosome analysis.

Nucleic acids research ·Vol. 36 ·No. Database issue ·2008-01-00 ·Pages D178-83

Piekna-Przybylska D, Decatur WA, Fournier MJ

Abstract

The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3D maps for other organisms. Data are provided for human and plant (Arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and eukarya. Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis. Displaying positions of modified nucleotides is fully manageable. Views of each modified nucleotide are controlled by individual buttons and buttons also control the visibility of different ribosomal molecular components. A section called 'Paint Your Own' enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known. This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins. The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/

MeSH Terms
Computer Graphics Databases, Genetic Humans Internet Models, Molecular RNA, Ribosomal/chemistry Ribosomes/chemistry Software User-Computer Interface
Chemicals
RNA, Ribosomal
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Piekna-Przybylska Dorota
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.
Decatur Wayne A
Fournier Maurille J
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkm855
Published
2008-01-00
Epub
2007-00-18
Pages
D178-83
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2238946
Subset
IM
Grants
NIGMS NIH HHS · R01 GM019351 · United States
NIGMS NIH HHS · GM19351 · United States
External Links
PubMed source DOI: 10.1093/nar/gkm855 PMC Full Text View journal details
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