say SMILES!

Recently, Babel (in my system) was not working and I needed to convert my .sdf files to smiles format. I troubleshooted the error was able to run successfully. But, this made me think, what about a web-based application to do this format conversion? That’s how I found these three amazing tools based at the National Cancer Institute’s CADD Chemoinformatics group.

1. Online SMILES Translator and Structure File Generator

http://cactus.nci.nih.gov/translate/

Upload your .sdf file and get the SMILES format in Kekule or Aromatic format. Also, converts .sdf file to .pdb, .smiles, and .mol. Although, it does not have all the file formats listed in Babel. For a quick conversion, this is amazing site.

2. Create image files without any molecular visualization tool.

http://cactus.nci.nih.gov/gifcreator/

This was a cool site. Just put a smiles format and see the many colorful images you can make with your structure. Not only that. If you wanted to know what atom number is that Carbon next to the Nitrogen, make sure to have the “Image Map Style” to “Atoms”, similarly to see the connectivity by selecting “Bonds”. Simultaneously, if the generation of an HTML image map associated with the image is desired, just copy the code below. See details here

gifgen000N9XrBT

3. Image-to-Structure file-conversion

Found a cool structure in a book and tired of drawing that on a structure editor? This is the site for you, then. Scan the page and upload the image and see the transformation happening! And click on the “Show 3D” to see the image on paper coming as a 3D structure that you could download it as a .sdf file.

http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi

See the screenshot of the image to above image to the structure

Screen Shot 2013-04-16 at 6.45.18 PM

Click to see full-size

References:

ResearchBlogging.org
Weininger, D. (1988). SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules Journal of Chemical Information and Modeling, 28 (1), 31-36 DOI: 10.1021/ci00057a005

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