The simple Mc-Annotate program analyzes a RNA structure and identifies the following components of the structure:

  • Sequences (and annotation: parenthesis for helices, b for base-pair and X for tertiary base-pair), e.g.:

  • Residue conformations
  • Base-pairs and the structural elements that interact
  • Base triples
  • Adjacent interactions (stacked, paired or not)
  • Non-adjacent stacked interactions
  • Helices (bulges of length 2 or less are accepted and indicated by a number):

  • Strands (single-strands, loops, hairpins, bulges)
  • Pseudoknots

You can submit a RNA structure in ASCII PDB format (gzipped files are also accepted) by entering it here. Please be aware that all models from the file will be annotated, so that in this case, it may take a while to run.

Note that this may take a while. Please be patient!

Also, please note that a newer version of MC-Annotate can be downloaded here

Related links

  • Base pair classification (out-dated)
  • Mc-Sym molecular modeling software
  • Protein Data Bank