The Proteax module of iScienceSearch provides an easy way to perform substructure and structure similarity searches in major Internet databases containing peptides, such as PubChem, CheBI and ChemSpider starting from plain 3-letter-code peptide sequences.

When performing real structure searches, you can find peptides containing structure modified amino acid residues. These cannot be found using strictly text based searches such as BLAST.

You can also search generic text terms in PubChem and CheBI and end up on a result page that only contain structures that are peptides or peptide like structures such as Penicillin.

In order to analyze the results easily, we transform the complex structures back into the 3-letter-codes. We show structures when we cannot map back to the natural amino acids, see the picture below.

Publications:

Finding unusual peptides on the internet using plain three letter sequence codes (Alexander Kos and Hans-Jürgen Himmler), see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606151/