Related RNA Databases
the SSU rRNA modification database
A compilation of posttranscriptional modification sites in RNA from the small ribosomal subunit. Includes identities of modified nucleosides if known, and provision for comparison of modifications in aligned sequences from Bacteria, Archaea and Eukarya.
tRNAdb: Compilation of tRNA sequences and tRNA genes
This extensively revised collection contains 623 tRNA sequences and 12,000 tRNA genes, classified by amino acid specificity. Provisions include graphical representations of their secondary structures, a customizable output of aligned or unaligned sequences, and a variety of search criteria.
Web sites, including databases, dealing with RNA transcription, processing, editing and other aspects of RNA metabolism.
AMBER force field parameters
The website from John Santalucia's group (Wayne State University) contains AMBER parameters for all 103 modifications known to exist in RNA. The links to each one of the modifications contain downloadable AMBER parameter files and the input and output files used in developing the parameters.
Protein Data Bank with 3D structures of a number of modified nucleosides
This link leads to the PDB accession codes to the RNA structures containing the modified bases.
- Amber force fields of all modified bases appearing in yeast tRNA-Phe
Yeast snoRNA Database
Small Nucleolar RNAs (snoRNAs) from the Yeast Saccharomyces cerevisiae. A comprehensive database of S. cerevisiae H/ACA and C/D box snoRNAs, with numerous links to snoRNA and other databases.
The 3D rRNA modification maps database
The 3D maps database allows visualization of modification sites in the five ribosome and mRNA and tRNAs for several model organisms and permits users’ construction of 3D maps for other organisms.