Archive for the Natural products Category

Recently I heard someone who cycled the 1400 km from John O’Groats to Lands End, with a headwind all the way, because it looked on the map as if it was downhill and hence easier. (I am grateful to Neil Swainston of the University of Manchester for this anecdote.)

You might think that “down” on the page is unlikely to be “down” in 3D space, but there is an interesting exception to this, at least for certain interpretations of “down”. (more…)

I’ll be talking at the 6th Joint Sheffield Conference on Cheminformatics in July on Validation and Standardization of Molecular Structures in General and Sugars in Particular. This is a taster.

Sugars in Particular

One of the big problems with chemical structure algorithms is that they can’t, in general, cope with the ways that chemists are accustomed to drawing sugar molecules. They will lose the stereochemistry around the sugar ring, collapsing D-glucose, say, on to L-glucose, not to mention allose, altrose, gulose and all the others.

(ChemDraw, I should note, can interpret chair stereo properly, but it is very much an exception.)

The first step in determining correct stereochemistry for a chair atom is recognizing a chair hexagon. That is the subject of this post.

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Do you know about Natural Product Updates?

Natural Product Updates (NPU) gives you the molecules involved in key developments in natural product chemistry. Thanks to our work in interpreting what chemists mean, not just what chemists draw, ChemSpider now links to NPU’s data for 13800 natural products since 2005, of which 7800 are brand new to ChemSpider.

Where ChemSpider has information on a compound in NPU you will see the image above, as in, for example, calothrixin B. This is a link to NPU page on the RSC Publishing Platform.

Soon we’ll be integrating more of our graphical databases into ChemSpider. Watch this space!