Volume 5 Supplement 1
Finding unusual peptides on the internet using plain three letter sequence codes
© Kos and Himmler; licensee BioMed Central Ltd. 2013
Published: 22 March 2013
Finding peptides with modified amino acids is difficult or impossible when you use plain three letter sequence codes and BLAST. You can find those peptides when you use the structure as a query, but drawing the structure correctly is rather difficult for non-chemists. We developed CWM Global Search  with Proteax . This is an Internet search engine that allows scientists such as biologists to input plain three letter sequence codes and subsequently search the corresponding chemical structures on the Internet including substructure searches and structure similarity searches.
The results are mapped back to three letter sequence codes if possible. This makes the interpretation of the search results much easier than trying to interpret the structures or systematic names normally provided in the databases. Results can also be easily compared using "Proteax for Spreadsheets".
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.