The services page at ChemSpider offers a number of valuable capabilities for chemists. For those of you working with amino acids you might be interested in having an easy way to convert an amino acid sequence to a chemical structure. The services page allows you to do this. Simply enter the sequence using the usual three letter amino acid codes as a string and click on Convert to Structure to generated the chemical structure associated with the sequence. The structure can then be downloaded to the desktop as a molfile and opened up in your standard structure editor. If you do not have a structure editor download the ChemSketch Freeware. The image below is generated by typing Gly-Trp-Glu in the dialog box.

aMINO ACIDS

From this point you can generate properties or search the structure in ChemSpider. the same general approach is true for chemical names and other identifiers. Input a chemical name, InChI code, SMILES string and convert to chemical structure. These capabilities are delivered using the strengths of the ACD/Name to Structure package provided by our collaborator Advanced Chemistry Development. Enjoy!

Stumble it!

One Response to “Did You Know? NUMBER ONE – Creating Structures from Amino Acid Sequences”

  1. David Bradley says:

    Building peptides has been one of my big bugbears over the years. With various drawing packages, and working to tight copy deadlines, I have never found the time to get to grips with how to do them properly and make them look like properly laid out 2D structures. I have always ended up with a tangled mess in the past and simply resorted to clipart.com to get some generic picture related to the article in question. Next time, I just created a test synthetic peptide Gly-Trp-Glu-Phe, saved it as a mol file, opened it in ChemSketch produced an optimized 3D version, imported it into Crystal Diamond and rendered it with Pov-ray, although I left out the clouds and chequered reflections. You can see my efforts here. Now all I need to do is find a news story about this mock peptide with which to illustrate it…

    db

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