Your Favorite Chemical Spreadsheet

September 12, 2008

On a recent article describing ChemPhoto, Oleg Ursu commented:

This looks a lot like Marvin View from ChemAxon (I am not sure about the details), which I have been using a lot lately.

Although the appearance is similar, the purpose is different. MarvinView is in a category of desktop cheminformatics software called "chemical spreadsheets." A chemical spreadsheet displays multiple chemical structures in a regular arrangement (typically grids or rows) for the purpose of manipulating them in the same ways as text and numerical data can be manipulated in spreadsheet applications like Excel (sorting, performing calculations, charting, editing, etc.).

Although ChemPhoto uses the grid metaphor to display structures, it's not a spreadsheet. It doesn't do analysis. It doesn't even allow editing of the underlying document. It's sole purpose is to display large numbers of structures for the purpose of modifying their appearance and imaging them. ChemPhoto assumes you've created an SD File with your chemical spreadsheet (or Web service) of choice.

But Oleg's comment got me thinking again about chemical spreadsheets.

Back when I started out as a medicinal chemist in 1999, there were few chemical spreadsheets. Today, the category has become very crowded. Between my own personal experience and just a little bit of research, I've come up with ten different chemical spreadsheets. They are, in no particular order:

  • MarvinView Cross platform and free for evaluation.
  • Seurat Cross-platform database connectivity and SAR analysis.
  • Bioclipse The only open source member on this list. Project-centric perspective.
  • DIVA The first chemical spreadsheet that I actually enjoyed using. Doesn't seem to be actively marketed anymore.
  • Accord An Excel plug-in that, at least in its earlier versions, was very cumbersome.
  • Third Dimension Explorer The most feature-rich chemical spreadsheet I've used. Support for many forms of sophisticated visual analysis geared specifically toward drug-discovery programs. Developed in-house at Johnson & Johnson.
  • Spotfire Feature-rich but difficult to learn. Cheminformatics built on top of a general purpose analysis engine.
  • ICM Don't know much about this one.
  • quattro/DS The name sounds similar to the Quattro Pro spreadsheet, but as far as I can tell, this is the only connection.
  • ISIS Spreadsheet functionality focused on creating and maintaining databases.

I'm sure this list is incomplete. If you know of others, please feel free to post a link. If you have a favorite (or least-favorite) chemical spreadsheet, what is it and why?