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Tag Archives: Computer Assisted Structure Elucidation

Our article Structure Revision of Asperjinone Using Computer-Assisted Structure Elucidation Methods

Our article “Structure Revision of Asperjinone Using Computer-Assisted Structure Elucidation Methods”, is now available on the Journal of Natural Products website here.

ACS_paper

This was a long time coming…almost a year in the review process and iterations. I continue to see the reports from many publishers about how fast articles are published but my experience in 2012 is that it is many months past the published averages! The primary hurdles appear to be the speediness of reviewers and the willingness of editors to pursue them! When I ask for updates the general response is “We will contact the reviewers…”

The URL http://pubs.acs.org/articlesonrequest/AOR-IKzXYYSAAQCbXVAc4Fva can be used for us to distribute 50 e-prints of the article so please feel free to grab one. Details below…

“As part of the ACS Articles on Request e-prints service, ACS authors may choose to e-mail or post this link on their website to distribute up to 50 free e-prints of their final published articles to interested colleagues during the first 12 months of publication. After that 12-month period, any author’s article may be accessed without restriction via the same author-directed link that appears above. The link seamlessly directs subscribers to the full text version of the article on the ACS Publications website.”

 

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Our Contributions to the Literature Regarding Computer-Assisted Structure Elucidation

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

 

 

 

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Who sets the price for our book and why does it vary so much?

I have written a lot of book chapters over the years, probably about 20, and have another 4 in press . I also have 3 more waiting on me to write by end of year (agh…). I have co-authored three books¬†over the past few years (1,2,3) but other than the first book, self-published with ACD/Labs, I was not involved with setting the price. That’s probably good as it would likely be randomly changed, as would the list of authors and the number of pages!

There has been a question on this blog about whether I think the price for the most recent book is appropriate and I will discuss that when I have more time. I¬†would say that based on the likely number of copies that will sell for this very specialized area, the size of the book and the amount of work it took us to put together (almost 2 years of work describing about 15 years of work), that this is probably a fair price…about $220 (but with price variation to be discussed below). If you consider that our single articles can be $30-35 for ONE PDF for 48 hours of access summarizing only one point in time in our research then I do think that the price is fine. Having previously “self-published” and seen how many books can be sold in that way I’d say that price is definitely appropriate considering the quality of support we have received from the publisher, RSC, and the associated costs of set-up for printing that must be taken on. Maybe self-publishing would be better nowadays¬† in terms of increased volume of sales, as my last experience was 10 years ago, but based on comments from people using Lulu.com (for chemistry books), sales volume is very low and for worldwide marketing to libraries a professional publisher IS necessary.

Back to the point of this blog post. Who really sets prices for a book, taking just the chemistry book I am involved with as an example? Amazon want about $220, at present, for a copy of our book. That includes a “random 7% discount” that comes from where? However, then things get interesting….

Note that the author listing order for our book is: Mikhail Elyashberg (Author), Antony Williams (Author), Kirill Blinov (Author). Now then….

Borders sell it for $424 here and change the author order to by  Antony Williams,  Mikhail Elyashberg and Kirill Blinov.

BetweenReads.com.au have the price listed in Australian dollars, add the book editor as an author, change the order of the authors and add another random discount.

PowellsBooks loses two of the authors and leaves only Mikhail Elyashberg as the sole author but keeps the price as the original Amazon price, no discount.

Barnes and Noble give a 19% discount before the book is even released, not an uncommon situation of course.

In most cases the number of pages is underestimated to be 368 pages but if you consult the RSC page you will see that it is almost 500 pages and the LIST price is 146.99 UK Pounds.

Who knows where these various online book sellers get their information and how their prices get set, but clearly there are discrepencies. While this book isn’t a mainstream novel moving the basic info out to the sites should be easy. One has to assume that the various discounts are based on either the scale of the sales operation or, it seems, more random factors. All very interesting…and no resolution from me!

 

 

 

 

 

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Our book published Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation

Almost two years of work, a collaboration and friendship developed over many years of my tenure at Advanced Chemistry Development¬†(with Mikhail Elyashberg and Kirill Blinov),¬†a story about a decade of work to develop what we believe is the world’s premier Computer Assisted Structure Elucidation software, and multiple iterations later, our book is now at the printers.

Our Book COver

Our book is “Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation” and is already listed on Amazon here.

“Computer Assisted Structure Elucidation (CASE) systems are powerful software applications capable of outperforming human data interpretation in terms of both speed and reliability. They combine software algorithms with tools for molecular structure elucidation using spectroscopic data. This book describes the principles on which CASE systems are based and concisely explains the algorithmic concepts behind the programs. It puts the technique in the context of its origins and describes the challenges that have been overcome to produce modern CASE systems. It uses the authors’ software development experience to discuss the present state-of-the-art and explains how the synergistic marrying of man and machine can provide superior results. Readers will gain a firm grounding in the fundamentals of CASE, an understanding of the challenges associated with algorithms, and an appreciation of the technologies underlying NMR prediction and structure verification. Scientists who have never used CASE systems before will find all the information necessary to master this new and very effective approach. Those with some experience will benefit from details on the latest developments.”

I willingly admit I’m glad it’s over…it feels great to have it finished, great to know its at the printers and good to know that we have likely written the definitive volume in this area for the time being. Now time to let my eyes recover before getting back to writing two more volumes about NMR applied to Natural Products, to be released next year all being well!

 

 

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