Digital features in the Journal of Medicinal Chemistry

J. Med. Chem. has an editorial describing how the journal plans to make structural information in papers more accessible in a digital format. Most of this would entail having spreadsheets of compounds with SMILES strings supplied along with the paper. I applaud this effort since the ability to view and manipulate structures in 2D and 3D is one which chemists have long coveted but not realized until now.

With this issue, therefore, the Journal of Medicinal Chemistry embarks on an initiative to integrate the chemical information it publishes with digital media and chemical software. The first step in this effort is the linkage of articles with molecular formulas in a format that can be generated by and read into chemical software. The immediate benefit is that readers will be able to transfer compounds from articles into chemical drawing programs, databases, and computational tools. In the near future, this association of articles with computer-readable chemical formulas will provide a foundation for the creation of new journal features that will bring chemistry to life on the Web and in digital readers and tablets. 

Authors are invited to use their existing chemical drawing programs (e.g., ChemDraw, ACD ChemSketch, Marvin Sketch) to generate a computer-readable SMILES formula for each compound presented in their articles. These formulas are then pasted into a simple spreadsheet, along with basic information about each compound. Ideally, this spreadsheet will provide a machine-readable version of the key data presented in the article’s tables. 

Ideally I would like a PDF manuscript to be fully interactive. You should be able to right-click on a protein structure and be able to directly view it in the PDB. Better still would be an ability to rotate and zoom in on the 3D structure inside the PDF format in real time. A similar capability for small molecules would also be immensely useful; being able to look at structural parameters (bond lengths, angles etc.) and conformations extracted from manuscripts in real time would be quite enabling. We aren't there yet but I have little doubt that it's only a matter of time. This is a propitious beginning.