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July 12, 2007

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It's been interesting following the discussion about the various NMR prediction softwares. But I wish you could include other programs/packages as well such as:

ChemDraw's built in 1H/13C estimation
The Perch tools incorporated into TopSpin
... and others which I might not be aware of

In my opinion a review of the all programs available for NMR prediction would be very interesting reading. Perhaps one is available already?

Egon Willighagen

Funny quote: "Of course customers are really interested in how accurately a prediction program can predict THEIR molecules - not a collection of external data such as NMRShiftDB.”

Sure, they know what THEIR molecules are :)

It is interesting to realize that the NMRShiftDB allows you to upload your molecules, or alternatively, you download the software (it's open source) and the data (it's open data) if you don't want to send your molecules over the internet, and the NMRShiftDB software will automatically take into account your own data set.

Thus, if you are working on a series of related molecules, you can extend the NMRShiftDB data set with already elucidated structures, reducing the prediction error for your yet related unknowns derivatives. It is that easy to include prior/expert knowledge in the NMRShiftDB.

I believe the ACD/Labs software allows this too, so the quote is really meaningless. Not correct, not wrong, simply says nothing.

Ryan

Hi, and thanks for the comments.

In regards to prediction comparison to other products. I would love to have the opportunity to do that. Unfortunately, it is not always possible for me to get access to a specific software packages (especially considering I am employed by a "competitor"), and further it isn't necessarily that fair for me to generate predictions in another vendor's software until I am properly trained in all of their options.

One of the reasons I have been so excited about the NMRShiftDB is because it is open access, it allows anyone to download the SDF file and run it through their predictions for validation. For that reason it should be quite easy for Cambridge Soft and the Perch tools to do the same that both ACD/Labs and Modgraph have done to this point. If they are willing to do that and share those results, I would be happy to share them on my blog provided the study was conducted correctly.

FYI, ACD/Labs has an older comparison between ACD/HNMR and CNMR Predictor vs. Cambrige Soft's ChemNMR on their website.

http://www.acdlabs.com/products/spec_lab/predict_nmr/chemnmr/

Beware however, it is an older comparison from probably about 3 years ago and I am sure both ACD/Labs and Cambridge Soft's predictions have improved significantly since then. Also please note that this was a dataset compiled in-house by ACD/Labs using a leave-one-out analysis.

I think a better comparison would come from Cambridge Soft downloading the SDF file from the NMRShiftDB and generating a prediction error on their own. This would ensure a result from the most recent software packages.

I am of course not issuing a challenge, I just think it would be the best way to accurately compare this package with others.

Ryan

Hi Egan, and thank you for bringing up a very important point, one regarding prediction training. Of course if users add their own data to the prediction engine,it will improve the predictions on THEIR molecules. This feature has been available in ACD/Labs NMR predictors for years, and is also available in Modgraph's NMRPredict.

However users can only add already elucidated structures to their databases in order to improve the predictions. I think when Jeff and I refer to "THEIR" molecules, we are referring to the end-users molecules that have not yet been elucidated (and thus not yet trained)

This is why I believe the prediction accuracy value on the subset of novel chemical shifts (1.74) is the most relevant to an end-user because it doesn't take into account those chemical structures that are already in the database.

So in the end, I don't believe the quote is meaningless.

Malcolm Beckett

This is great openness and transparency is what I want, not my Dad is bigger than your Dad arguments seriously the most important aspect of this discussion is that we learn and are open to new ideas thanks to both Jeff and Ryan for the debate. In anticipation that this will hopefully be discussed again in a few years time

Ryan Sasaki

Hi Malcolm,

Thanks very much for your comments! It is my sincere hope that openness and transparency serves as the foundation for this blog. I am glad you have found the debate both useful and interesting.

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