RSS

Dictionary Lookups and Optical Structure Recognition Versus Structure Drawing. Which is Less Error Prone?

02 Oct

Luqidcarbon has put up a recent blog posting about the speed by which he/she can draw structures in ChemDraw and asked for challengers. PRM has commented in Chemical SpeedDrawing. The challenge is outlined below…

Liquid Carbon

A few people took the challenge and commented on the blog posting. Me too, but I cheated.

I’m of the opinion that for “KNOWN” structures the best thing to do would be to “look it up” in an appropriate reference collection. Now, I could go to ChemSpider for all of them (or PubChem) but I can predict that because the curation process is not as advanced as I would like it to be we will have issues with multiple structures with the same connectivities but with different stereocenter definitions (incomplete in general). Just to check I did so…

THC is there but a search on THC turns up three structures. Since we’re trying to reproduce the right one we can visually inspect and download. Takes me about 20 seconds to locate, inspect and download into my drawing package

Penicillin G…little more complex because there is more stereochemistry to inspect. ChemSpider gives 5 hits, 1 is now curated out since it’s a dimer. 1 is a potassium salt and the other three have the right connectivities but different stereo displays…easy to download one and change the stereo to match the structure of interest..about 30 seconds.

(+)-Discodermolide gives 6 hits..all differing in their stereochem. Nevertheless….I can download the structure and edit the stereo in about half the time. The correct structure on ChemSpider is here, with the InChIKey AADVCYNFEREWOS-USOWQXFZDY.

What’s the message?..it MAY be faster to download the “framework” and match the steroechemistry in the drawing you are trying to copy rather than draw from ground zero. Why? Notice the structure of discodermolide drawn by liquidcarbon is WRONG as far as I can tell….see below for the detail but there is a methyl instead of a hydroxy on his/her structure.

Rather than use ChemSpider I went to a HIGHLY CURATED data set of names and structures called the ACD/Dictionary (Don’t forget I used to work at ACD/labs so am biased to this product since I managed it. That Ssaid, it is VERY well curated…thousands of hours of work!). It’s included with a copy of the commercial ChemSketch. There are alternatives on the market, for example ChemDraw could likely reverse all the names above to the appropriate structures but I don’t have the software to check. But, bottom line, there are faster ways for “known structures” than redrawing.

ChemSketch dictionary

Fifteen seconds TOTAL is what it took me to put the structures for all three on a page. Oh, and it had the OH in place as shown. What’s this error in structure worth to you in terms of time and proliferation? A chemist costs at least $150 per hour. If the incorrect structure proliferates from misdrawing whet will it cost a company??

A drawing package like this is a few hundred bucks for corporate and just over a hundred bucks for academia (see here). By the way…I am NOT on commission…but I’ll take COFFEE!!!! ChemDraw has nam-structure conversion too as does ACD/labs and they can all convert common names to structures..with differing degrees of accuracy.

So, forget the redrawing when there are other solutions for “knowns”.

What about for unknowns…when you are looking at a NEW structure in a paper, or on a website and it’s complex …should you redraw? NO, NO, NO.

I have blogged previously about software for converting structure images to real structures (connection tables). Today I had the pleasure of sharing space with Stephen Boyer from IBM who originally patented scan and convert for chemical structures. I am interested in the possibility of using BATCH processing of structure images to convert structures from Open Access articles and adding them to ChemSpider. We have access to 50,000 Open Access articles…and lots of structures therein. If we can batchwise convert then we can populate the database and index by structure.

With this in mind I have started working with Simbiosys to test and validate their CLiDE software. My first tests give pretty good results and I am only in “learning mode”. I have just taken delivery of a beta version of their latest software and am yet to install so I asked them to grab the image from the webpage and convert. the results are below.

CLiDE

The conversion to connection tables lost a couple of stereo bonds BUT the connection itself is there and it is EASY to put the stereo back in. Plus, it lost a proton on THC but that is easy to add back in. That’s pretty impressive!

Now imagine a work flow where all you do is open up a PDF file, activate CLiDE, select the structure with a rectangular drag and it recognizes and converts to a connection table and all you do is check it and ‘touch it up”. That 150 seconds of drawing time that liquidcarbon talks about could be reduced to about 30 seconds AND, hopefully, no hydroxyls will be lost.

I am definitely putting effort into CLiDE validation at present as it appears to be well-advanced but not yet perfect (hey, it’s software!). I WILL be supporting their efforts to make it better…I want to use it for my own selfish needs and I judge it is performing well. I’ll keep you informed.

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
Leave a comment

Posted by on October 2, 2007 in Uncategorized

 

0 Responses to Dictionary Lookups and Optical Structure Recognition Versus Structure Drawing. Which is Less Error Prone?

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

 
Stop SOPA