For those who haven’t encountered it yet, chemicalize.org is a tool for adding chemical information to your web browsing – and it’s free! Provided by the chemistry software company, ChemAxon, under a Creative Commons license, chemicalize can convert chemical names to structures – either on a query basis or converting an entire web page. In addition, ChemAxon have now added a page of calculated properties that can be accessed by clicking the generated 2D structure.
The tool will convert trivial chemical names such as saquinavir, as well as IUPAC names such as 7-chloro-1-methyl-5-phenyl-3H-1,4-benzodiazepin-2-one. Structure generation is based on ChemAxon’s name-to-structure software, although conversion of trivial names presumably relies on a database. I don’t know how comprehensive the database is, but it can certainly generate some interesting results when converting a web page – I hadn’t realised that trigger was a trivial name for something!
When a web page is converted, recognised structures are underlined in the text. Hovering over the underlined text produces a tooltip with the 2D structure of the molecule and this can be clicked to visit the calculated properties page. The properties page provides a variety of useful information including, logP, rotatable bond count, pKa etc. The layout of the properties page can also be adjusted by the user, with some standard layouts provided for medicinal or synthetic chemist.
You can see the chemicalized version of this post here and visit chemicalize.org for further information.
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Just to let you all know that we have added chemical search to the chemicalize.org site.
The search let’s you draw, upload a structure or name a molecule as input and perform various structure searches (substructure, exact match and similarity) against the structures identified from web pages already ‘chemicalized’ by users and see the resulting structures (with the query highlighted in the result).
From each result structure you can go on to see a list of web pages where the target structure was included. An elegance is that you can also see other structures on the listed pages and select popular or diverse selection, to understand if the page is chemically relevant before you visit the link. Feedback from test users was very positive especially because they can chemically search ‘a significant proportion’ of Wikipedia.
Other features added include: Auto-complete, structure images for all auto-complete names and roll over large versions of structure images. The name to structure parser is also improved to increase conversion rate and remove error.
For more information see this demo video at the site or this presentation of chemicalize.org and the underlying technologies used from our recent US UGM.
Hope this is useful
Alex Allardyce: ChemAxon