Saturday, October 31, 2015

So, now you have SMILES that are faulty... visualize them?

So, you validated your list of SMILES in the paper you were planning to use (or about to submit), and you found a shortlist of SMILES strings that do not look right. Well, let's visualize them.

We all used to use the Daylight Depict tool, but this is no longer online. I blogged previously already about using AMBIT for SMILES depiction (which uses various tools for depiction; doi:10.1186/1758-2946-3-18), but now John May released a CDK-only tool, called CDK Depict. The download section offers a jar file and a war for easy deployment in a Tomcat environment. But for the impatient, there is also this online host where you can give it a try (it may go offline at some point?).

Just copy/paste your shortlist there, and visually see what is wrong with them :) Big HT to John for doing all these awesome things!