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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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May 4, 2010

Another Proposal For the Scientific Literature

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Posted by Derek

I was talking with a colleague yesterday, and I suddenly had an insight into an opportunity in scientific publishing. We were discussing the various computational/modeling papers that you see out in the literature. Some of them are quite interesting, many are worth looking at if it's your particular field - but many others are, well, not so great. I should mention up front that the same objections apply - and how - to the non-computational literature, of course. But there are a number of second-tier (and lower) journals to soak up those sorts of papers in the other disciplines.

What surprises me is that there's no Computational Chemistry Letters or some such. Communications in Computational Chemistry? CADD Comm? This would be the dumping ground for the piles of unconvincing computer-driven stuff that gets sent around by people who have paid a bit too much attention to the sales brochures that came with their software packages.

The barriers for entry to such things have been getting lower and lower, while the real state of the art has been getting more and more complicated. That's created a gap into which too much stuff falls. Who will speak for the bottom-dwelling "We modeled it, therefore it's real" constituency? The advent of systems biology has created more opportunities than ever for these folks. Isn't it time that there was an expensive, low-impact, completely disregardable journal for them, too?

Comments (13) + TrackBacks (0) | Category: In Silico | The Scientific Literature


1. Wavefunction on May 4, 2010 10:41 AM writes...

I completely agree. There's too much stuff these days in everything from JMC to CMC consisting of some fancy sounding neural network or graph theory analysis of drugs or proteins that's too abstract and complex for medicinal chemists to understand. More importantly, these studies often do a pretty poor job of even hinting at any causal relationship between the principles and the purported results. One keeps on wondering if the supposed good results arose just by chance.

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2. Sean on May 4, 2010 10:59 AM writes...

Good idea.

I agree that modeling has its place, but often wonder about the errors in protein modeling. I know their inputs have errors which seem to disappear when modeled.

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3. DrSnowboard on May 4, 2010 11:01 AM writes...

What, you don't like million compound virtual screens which ping out 4-5, 10micromolar hits? All rhodanines, or furyl imines or nitro phenols?
You luddites.

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4. HelicalZz on May 4, 2010 11:22 AM writes...

Elsevier considered this a few years back .... but it didn't fit with their marketing model.

Que sera


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5. p on May 4, 2010 1:15 PM writes...

The map is not the territory.

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6. 8020chemist on May 4, 2010 2:50 PM writes...

Journal of Molecular Graphics and Modelling

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7. Sili on May 4, 2010 3:26 PM writes...

Sounds like an excellent topic for arXiv. It's pretty much physics, anyway.

(Yes, I know that's just preprints, but I think it's a great ressource, and I hope chemistry adopts it eventually.)

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8. Computationally entertained on May 4, 2010 4:10 PM writes...

How about a journal for stuff that didn't work, in any disciplines?

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9. Anonymous on May 4, 2010 5:03 PM writes...

#8: But there is one:

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10. hypnos on May 5, 2010 1:17 PM writes...

Journal of Molecular Graphics and Modelling was already mentioned, Journal of Chemical Information and Modeling is also a good source of obscure publications.

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11. Wavefunction on May 5, 2010 2:51 PM writes...

@10: Yes, but JCIM also has many good ones
@3: Not all comp chemists are ignorant about these scaffolds. Certainly the ones I know are not.

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12. Computationally entertained on May 6, 2010 8:20 AM writes...


what I meant is a journal for failures from which useful things can be learned.

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13. LeeH on May 7, 2010 10:08 AM writes...


Journal of Chemical Information and Modeling has "obscure publications" the same way JACS has "obscure" articles on the newest synthetic reagent or reaction.

On the other hand, I agree with the gist of this thread. Most modeling method papers, unless they are clearly illustrated by experimental results or are especially instructive for the average medchemist, belong in a journal like JCIM or J. Molec. Graph. Mod.

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