Comments on: An Inquiry Regarding How is ChemSpider Used …and is it Providing Value?

By: anonymous

anonymous — Wed, 23 Jan 2008 20:05:27 +0000

I use it to add structure info for compounds in our database that lack such info. The name-based searching is better than PubChem based on the number of positive IDs I have seen.

By: Antony Williams

Antony Williams — Wed, 23 Jan 2008 03:31:12 +0000

This info from Greg Pearl at ACD/Labs…

For the PSA calculations we implemented the Fast 2D PSA by Peter Ertl (J. Med. Chem., 43 (20), 3714 -3717, 2000.)

http://pubs.acs.org/cgi-bin/abstract.cgi/jmcmar/2000/43/i20/abs/jm000942e.html

By: Patrick Camilleri

Patrick Camilleri — Mon, 21 Jan 2008 21:43:17 +0000

I use ChemSpider regularly, and many thanks for providing so much information. However, Iam very interested to know what algorythm is used to calculate the polar surface areas of molecules. Are values quoted dynamic PSA or the topological PSA or QikProp?

By: Alan Smith

Alan Smith — Wed, 08 Aug 2007 18:24:38 +0000

Chemspider is a great database to follow up on unknown mass features from profiling experiments. I greatly appreciate the advanced search functions such as Search by Data Source which allows one to choose what database to search. I use this database to finish off putative annotations after mining in house databases. Its also great for assigning putative formulas to masses never mind the 1200 structures. Hopefully, the maintainers keep working to make this database more and more usable.

By: John Shockcor

John Shockcor — Wed, 30 May 2007 18:46:48 +0000

I use ChemSpider to identify endogenous and xenobiotic metabolites during metabolomic studies of complex biofluids. It is a one-stop-shopping site that has everthing I need. I typically search by properties for monoisotipic masses or formulas in specific databases using the search by source menu. This feature lets me customize my search and has been a most welcome addition. Like David I aslo now grab mol files for my own structure catalog.

I have recently seen comments from the UK about errors and issues with calculated properties in ChemSpider. I would like to say to the ChemSpider team THANKS and don’t allow hypercritical people to get you down.

By: Mike Lee

Mike Lee — Tue, 15 May 2007 19:49:27 +0000

My use of Chemspider is consistent with David Bradley. Aside from the fact that I can search and obtain information on chemical structures, the database is fast…. blazingly fast. The speed (and organization of content!) of the search engine that relates to my focus/interest has been valuable, particularly with regard to structure and the ability to quickly predict pharmaceutical properties.

I do find that the size and speed of the database is unique. I also value the opportunity to easily share information obtained from Chemspider with my colleagues.

By: David Bradley

David Bradley — Mon, 14 May 2007 14:39:59 +0000

I obviously use Chemspider on a regular basis while putting together the chemistry news section dubbed Spinneret. I’m writing about a hopefully wide variety of chemical topics for the news section and so when a small molecule name comes up, I simply tap it into the integrated search box in the Firefox browser, hit return and the pertinent entry pops up almost instantaneously. By, the way, more about popups on the Chemspider blog.

Once the results are up, a quick check that I have the right structure and then I can cut and paste the entry URL, embed the structure graphic, and cut and paste the InChI for the Spinneret post in question. The InChI entries are embedded using the inchi span class as discussed by Egon elsewhere, so are I believe presented in a search usable format.

I am also now using the ChemSpider site to grab MDL mol files that can be fed into whichever structure software I am using (whether that’s Crystal’s Diamond, for high-res 3D renderings with Pov-ray, or ChemSketch for standard 2D structures. Depends on whether the image is destined and whether it is for a tech audience or one that prefers high-gloss ball and sticks with clouds and reflections