Protein Explorer

Protein Explorer (ProteinExplorer.Org) was a free macromolecular visualization software package, written largely by Eric Martz from 1998-2006, that worked in the Firefox web browser. It was designed for students and educators, but because of its power and ease of use, was also widely used by researchers. In 2003, it won the Merlot Classic Award for Exemplary Learning Materials in Biology: "Protein Explorer has revolutionized the teaching of biology at a molecular level.".

Protein Explorer utilized the MDL Chime browser plugin (which does the interactive molecular rendering, much as the Jmol applet does in Proteopedia). Although free, Chime was not open-source, and had very little development in the early 2000s. There was never a Chime for Mac OS X, and even on Windows, getting Chime to work was occasionally problematic. Protein Explorer works fully only in the Firefox web browser and only in Windows. Because of these problems, and because one must download and install the Chime plugin in order to use it, Protein Explorer's use has been declining since about 2005, and its development ceased in 2007.

Protein Explorer was, at least in part, re-designed to use open-source Jmol by Bob Hanson (the major developer of Jmol in recent years). This version is available at Jmol.ProteinExplorer.Org.

Although Protein Explorer (Chime version) was somewhat fussy to get working, it had some powerful capabilities, unmatched in ease of use, that make it worth the effort for some projects.

• Flash movies introduced how to use Protein Explorer, and a One-Hour Tour gets you started.

• It had extensive help for beginners, as well as introductory information on protein structure topics useful to researchers. No other molecular visualization program had so much built-in information about the principles of macromolecular structure. This included an extensive Help/Index/Glossary.

• It did nearly everything you can do in FirstGlance in Jmol, but with greater flexibility, including identifying non-covalent interactions to any moiety (Contacts), and displaying salt bridges and cation-pi interactions. With the greater flexibility comes greater complexity, so FirstGlance in Jmol is even simpler to use.

• Protein Explorer enabled you to customize the display and coloring in a molecular view, just as do Proteopedia's Scene Authoring Tools. In contrast, FirstGlance in Jmol limits you largely to "canned" views.

• It could be downloaded and used off-line.

• Protein Explorer did a better job of reformatting the information in the PDB file header section into a compact yet intelligible format, and explaining the terminology involved (e.g. Resolution, R value and Rfree) than did any other macromolecular visualization package at the time.

• A clickable sequence listing showed the location of any residue in the 3D structure ("Seq3D").

• Its NMR/Animation control panel facilitated exploration and animation of multiple-model PDB files, with great flexibility and control. It generated an animation script, from menus and buttons, that ran in both Chime and RasMol. Running this script in RasMol saved each frame as a .gif snapshot file, and these could then be assembled into a multi-gif movie. Examples.

• Protein Explorer's MSA3D was able to color a 3D protein model by evolutionary conservation from a multiple-sequence alignment containing as few as two sequences. Although the ConSurf Server calculates evolutionary conservation with a greatly superior algorithm (and then colors the 3D model accordingly), it requires a minimum of five sequences.

See AlsoSee Also

• Chime
• FirstGlance in Jmol
• Molecular modeling and visualization software