RNA FRABASE -- database to search three-dimensional fragments within 3D RNA structures

What you can do:
Search for 3D RNA fragments within a set of RNA structures.
Highlights:
  • This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling.
  • The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a 'dot-bracket' notation.
  • As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the 'dot-bracket' notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs.
  • Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters.
  • The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs.
  • The RNA FRABASE is automatically, monthly updated and is also accessible at http://cerber.cs.put.poznan.pl/rnadb.
Keywords:
  • Molecular Models
  • Nucleic Acid Conformation
  • RNA
  • RNA structure
  • 3D fragments
  • 3D structure modelling
This record last updated: 04-30-2008
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