Field of Science

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.


  1. This doesn't have to be something done by the journal though, does it? Imagine software on your desktop that could examine an image containing a chemical structure, parse the image, covert it into a SMILES, and send it to your favorite 3D structure viewer. Or maybe you could click on the text name of a protein and it would search multiple chemical databases and pull up the full structure or other related data. None of this should depend on the journal supplying additional information to you and it should be doable with today's technology.

    1. Good point. A universal software tool that could do this for papers from any kind of journal would be better. Until then though it's good to have at least some journals paying attention to this.

  2. This is something we've been doing at Nature for several years. (full disclosure: this is my job)

    We have compound pages with 3D, CDX, MOL, and CML files; a link to the compound in pubchem; and SMILES and InChI data. Often the prep is displayed as well.

    Check it out:


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