Interactive graphics return to protein science

Abstract

Visualization of molecular images is an important means of interpreting structural and other data and of communicating scientific results in the field of protein science. Long-time readers of the journal Protein Science will recall that early issues of the journal were accompanied by a floppy disk containing graphical images in the pioneering kinemage format developed by David C. Richardson and Jane S. Richardson (The kinemage: A tool for scientific communication, Protein Science (1992) 1, 3-9.). Unfortunately, kinemages disappeared from Protein Science a decade ago. In this issue, a Commentary by Li and Palmer (Protein Science (2009) 18, 678-681) returns interactive computer graphics to Protein Science. This article incorporates interactive figures, based on the open-source Jmol package (http://jmol.sourceforge.net/), that are viewable using any World-Wide-Web browser through embedded links within the electronic version of the paper. These figures are of two types. First, authors can generate figures specially designed to enhance the information presented in the article (see below). Second, any Protein Data Bank (PDB) code quoted in the manuscript will be linked to the FirstGlance in Jmol viewer (http://molvis.sdsc.edu/fgij/index.htm). This will allow the reader to immediately and interactively visualize the structure in question. No additional files or programs need to be downloaded or installed on a reader's computer in order to view these figures. The molecular images can be manipulated, either using command options provided within the figures (which requires no knowledge of Jmol) or by opening the Jmol console window (which requires a modicum of familiarity with molecular graphics packages). Jmol has been adopted by a number of other journals and organizations, including ACS Chemical Biology, Biochemical Journal, and the International Union of Crystallography, as a platform for “enhanced” figures. The level of interactivity provided by Jmol is the major benefit over animations or embedded movies; of course, animations and movies prepared in standard formats, using for example other molecular graphics software packages, also can be included as supplementary material to a paper in Protein Science. Interactive figures in Protein Science are prepared by incorporating user-generated Jmol scripts and hyertext markup language (html) content into html templates. This hybrid approach simplifies the process of generating figures for new users, but provides flexibility for more expert authors. We emphasize that this initiative is continuing to be developed. The commentary of Li and Palmer is intended to provide readers with a flavor of the system that we have in mind. Feedback is welcome. During the initial “learning phase”, authors wishing to include interactive figures in their papers in Protein Science should contact the Editor for additional information. The re-incorporation of interactive graphics into Protein Science is a long-awaited return of the journal to its roots and an exciting opportunity for authors to augment the usefulness of their papers for readers.