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Our Contributions to the Literature Regarding Computer-Assisted Structure Elucidation

18 Sep

When writing a publication how many of us conduct complete literature searches? For those of us who do not have access to Scifinder how are we finding our literature? Probably through Google Scholar? When I write a paper I admit that some of my searches may be less than complete but I do try and stay informed in regards to what is going on in my domain. VERY occasionally I get feedback from reviewers pointing me to references that they feel I either ignored or was unaware of. Many times they are co-authored by the reviewer themselves…and it is pretty easy to figure out who the reviewers are ūüôā

Today I received an email in my inbox about the latest article in the Journal of Cheminformatics.¬†It is¬†OMG: Open Molecule Generator. The article is¬†here.¬†¬†The abstract opens with “Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, ¬†Open ¬†Molecule ¬†Generator ¬†(OMG), ¬†which ¬†for ¬†a ¬†given ¬†elemental ¬†composition produces ¬†all ¬†non-isomorphic ¬†chemical ¬†structures ¬†that ¬†match ¬†that ¬†elemental ¬†composition.”

Having been involved with Computer-Assisted Structure Elucidation for many years, having co-authored a book about it (here) and probably the definitive review article from the past 5 years (here) I would have assumed that our work would have been referenced. I was surprised to see that our work was not referenced while other CASE systems were. Articles we’ve issued over the past few years are below. I’ve gathered them here to point the authors to in case they want to reference any of them and missed them in the literatire search.

I am taking advantage of the fact that I can leave comments on the provisional manuscript¬†here¬†(what a great capability!!!) and will let them know about this list. it would be good to compare the performance of the OMG with the structure generator under ACD/Structure Elucidator sometime….

 

1) M.E. Elyashberg, K.A. Blinov and A.J. Williams, Computer-aided Molecular Structure Elucidation on the Basis of 1D and 2D NMR Spectra, Applied Magnetic Resonance, (May 2000)

2) K.A. Blinov, M.E. Elyashberg, S.G. Molodtsov, A.J. Williams and E.R. Martirosian, An Expert System for Automated Structure Elucidation Utilizing 1H-1H, 13C-1H, and 15N-1H 2D NMR correlations, Fresenius J. Anal. Chem., 369, 709 (2001)

3) G.E. Martin, C.E. Hadden, D.J. Russell, B.D. Kaluzny, J.E. Guido, W.K. Duholke, B.A. Stiemsma, T.J. Thamann, R.C. Crouch, K.A. Blinov, M.E. Elyashberg, E.R. Martirosian, S.G. Molodtsov, A.J. Williams, P.L. Schiff, Jr., Identification of Degradants of a Complex Alkaloid Using NMR Cryoprobe Technology and ACD/Structure Elucidator, J. Heterocyclic Chem. 39, 1241 (2002)

4) M.E. Elyashberg, K.A. Blinov, A.J. Williams, E.R. Martirosian, S.G. Molodtsov, Application of a New Expert System for the Structure Elucidation of Natural Products from the 1D and 2D NMR Data, J. Nat. Prod., 65, 693 (2002)

5) G . E. Martin, C .E. Hadden, D. J. Russell, B. D. Kaluzny, J. E. Guido, W. K. Duholke, B. A. Stiemsma, T. J. Thamann, R. C. Crouch, K. A. Blinov, M. E. Elyashberg, E. R. Martirosian, S. G. Molodotsov, A. J. Williams, and P. L. Schiff, Jr., Identification of Degradants of a Complex Alkaloid Using NMR Cryoprobe Technology and ACD/Structure Elucidator, J. Heterocyclic Chem., 39 1241-1250 (2002).

6) K. A. Blinov, D. Carlson, M. E. Elyashberg, G. E. Martin, E. R. Martirosian, S. Molodtsov, and A. J. Williams, Computer-Assisted Structure Elucidation of Natural Products with Limited 2D NMR Data: Applications of the StrucEluc System, Magn. Reson. Chem., 41, 359-372 (2003).

7) G. E. Martin, D. J. Russell, K. A. Blinov, M. E. Elyashberg and A. J. Williams, Applications and Advances in Cryogenic NMR Probes & Computer-Assisted Structure Elucidation. Ann. Magn. Reson., 2, 1-31 (2003)

8)¬†K. Blinov, M. Elyashberg, E. R. Martirosian, S. G. Molodtsov,¬†A. J. Williams, M. H. M. Sharaf, P. L. Schiff, Jr., R. C. Crouch, G. E. Martin, C. E. Hadden, and J. E. Guido, ‚ÄúQuindolinocryptotackieine: The Elucidation of a Novel Indoloquinoline Alkaloid Structure through the Use of Computer-Assisted Structure Elucidation and 2D-NMR,‚Ä̬†Magn. Reson. Chem.,¬†41, 577-584 (2003).

9) M. E. Elyashberg, K. A. Blinov, E. R. Martirosian, S. G. Molodtsov,¬†A. J. Williams, and G. E. Martin, Automated Structure Elucidation ‚Äď The Benefits of a Symbiotic Relationship between the Spectroscopist and the Expert System,¬†J. Heterocyclic Chem.,¬†40, 1017-1029 (2003).

10) M. E. Elyashberg, K. A. Blinov, A. J. Williams, S. G. Molodtsov, G. E. Martin, and E. R. Martirosian, Structure Elucidator: A Versatile Expert System for Molecular Structure Elucidation from 1D and 2D NMR Data and Molecular Fragments, J. Chem. Inf. Comput. Sci. 44, 771-792 (2004).

11) S. G. Molodtsov, M. E. Elyashberg, K. A. Blinov, A. J. Williams, E. E. Martirosian, G. E. Martin, and B. Lefebvre. Structure Elucidation from 2D NMR Spectra Using the StrucEluc Expert System: Detection and Removal of Contradictions in the Data. J. Chem. Inf. Comp. Sci., 44, 1737-1751 (2004)

12) G. J. Sharman, I. C. Jones, M. P. Parnell, M. C. Willis, M. F. Mahon, D. V. Carlson, A. J. Williams, M. E. Elyashberg, K. A. Blinov, S. G. Molodtsov. Automated structure elucidation of two products in a reaction of an a,b-unsaturated pyruvate. Magn. Reson. Chem. 42, 567 (2004)

13) Y. D. Smurnyy, M. E. Elyashberg, K. A. Blinov,  B. A. Lefebvre, G. E. Martin, and A. J. Williams, Computer-Aided Determination of Relative Stereochemistry and 3D Models of Complex Organic Molecules from 2D NMR Spectra, Tetrahedron, 61, 9980-9989 (2005).

14) M. E. Elyashberg, K. A. Blinov, A. J. Williams, S. G. Molodtsov, and G. E. Martin, Are Deterministic Expert Systems for Computer-Assisted Structure Elucidation Obsolete? J. Chem. Inf. Model. 46, 1643-1656 (2006).

15) M. E. Elyashberg, K. A. Blinov, S. G. Molodtsov, A. J. Williams, and G. E. Martin, Fuzzy Structure Generation: An Efficient New Tool for Computer-Aided Structure Elucidation (CASE), J. Chem. Inf. Model., 47, 1053-1066 (2007). 10.1021/ci600528g

16) M. E. Elyashberg, A. J. Williams, and G. E. Martin. Computer-Assisted Structure Verification and Elucidation Tools In NMR-Based Structure Elucidation. Review article. Progress in NMR Spectroscopy (2007) 10.1016/j.pnmrs.2007.04.003 

17) Y. D. Smurnyy, K. A. Blinov, T. S. Churanova, M. E. Elyashberg, and A. J. Williams. Toward More Reliable 13C and 1H Chemical Shift Prediction: A Systematic Comparison of Neural-Network and Least-Squares Regression Based Approaches, J. Chem. Inf. Model.  48, 128-134, (2008)

18) M. E. Elyashberg,¬†A. J. Williams, D. C. Lankin, G. E. Martin, J. Porco, W. F. Reynolds, and C. Singleton, Applying Computer-Assisted Structure Elucidation Algorithms for the Purpose of Structure Validation ‚Äď Revising the NMR Assignments of Hexacyclinol,¬†J. Nat. Prod.,¬†71, 581-588 (2008).

19) M.E. Elyashberg, K.A. Blinov and A.J. Williams, A Systematic Approach for the Generation and Verification of Structural Hypotheses. Magn. Reson. Chem. 47, 371-389, (2009)

20) M. E. Elyashberg, A. J. Williams, and K.A. Blinov, The Application of Empirical Methods of 13C NMR Chemical Shift Prediction as a Filter for Determining Possible Relative Stereochemistry. Magn. Reson. Chem. 47, 333-341 (2009)

21) Y. D. Smurnyy, K. A. Blinov, T. S. Churanova, M. E. Elyashberg, and A. J. Williams. Development of a fast and accurate method of 13C NMR chemical shift prediction. Chemometrics and Intelligent Laboratory Systems, 97(1), 91-97, (2009)

22) M. E. Elyashberg, A. J. Williams and K. A. Blinov, Structural revisions of natural products by Computer Assisted Structure Elucidation (CASE) Systems, Nat. Prod. Rep., 2010, DOI: 10.1039/c002332a

23) Blind trials of computer-assisted structure elucidation software, Journal of cheminformatics 4 (1), 5, A Moser, ME Elyashberg, AJ Williams, KA Blinov, JC DiMartino

24) ¬†Elucidating ‚Äėundecipherable‚Äôchemical structures using computer‚Äźassisted structure elucidation approaches, Mikhail Elyashberg, Kirill Blinov, Sergey Molodtsov, Antony Williams,¬† ¬†Magnetic Resonance in Chemistry,¬†50(1), ¬†22‚Äď27, ¬†2012¬†DOI:¬†10.1002/mrc.2849

BOOK: Contemporary Computer Assisted Approaches to Molecular Structure Elucidation by Kirill Blinov, Mikhail Elyashberg and Antony J. Williams, Royal Society of Chemistry

 

 

 

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‚Äô 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‚Äôs 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 ‚ÄúChemistry Dashboard‚ÄĚ 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.

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6 Responses to Our Contributions to the Literature Regarding Computer-Assisted Structure Elucidation

  1. Emma Schymanski

    September 24, 2012 at 10:09 am

    There is a nice extensive list of the MOLGEN-related work here:
    http://molgen.de/?src=documents/publications

    Not many of those turned up in Julio’s article either.

     
  2. Karen Salazar

    September 24, 2012 at 11:51 am

    Out of curiosity, have you done a comparison of the subjects used to index the articles cited vs. your articles? Could this be a case of the authors missing a particular synonym associated with this topic during their background research? Do you think that it is, perhaps, time for the creation of an official chemistry thesaurus in order to try to alleviate problems such as this?

     
    • tony

      October 3, 2012 at 9:18 pm

      Karen, I have not done such a comparison. It is possible that a chemistry thesaurus might be of value in helping but I must comment that when I use tools such as Google Scholar Citations, and get feedback from BioMed Central alerts that they are VERY efficient at providing me links to related papers. I am shocked that even a basic search on CASE and NMR didn’t turn up our papers…

       
  3. Emma Schymanski

    September 25, 2012 at 2:52 am

    “it would be good to compare the performance of the OMG with the structure generator under ACD/Structure Elucidator sometime”
    If you want to add MOLGEN (there are many versions) to the list, please let me know, I would also be curious. ūüôā

     
  4. Egon Willighagen

    October 1, 2012 at 6:36 am

    Antony, of those papers, which paper would most accurately describe the algorithm of the structure generation process used by ACD/Structure Elucidator?

     
    • Antony Williams

      October 1, 2012 at 11:29 am

      “Classic” generator which correspond to MOLGEN and OMG generators described in:
      Molodtsov, S. G., Computer-Aided Generation of Molecular Graphs, MATCH Commun. Math. Comput. Chem., 30, 213-224, 1994

      Generation on presence of set of nonoverlapping fragments (which used in “classic” generator too) described in:
      Molodtsov, S. G., Generation of Molecular Graphs with a Given Set of Nonoverlapping Fragments, MATCH Commun. Math. Comput. Chem., 30, 203-212, 1994

      Generator which takes into account 2D correlations and used in Elucidator is described in:
      S. G. Molodtsov, M. E. Elyashberg, K. A. Blinov, A. J. Williams, E. R. Martirosian, G. E. Martin, and B. A. Lefebvre, ‚ÄúStructure elucidation from 2D NMR spectra using the StrucEluc expert system: detection and removal of contradictions in the data.,‚ÄĚ Journal of chemical information and computer sciences, vol. 44, no. 5, pp. 1737‚Äď51, 2004.

       

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