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 has been, 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) is somewhat fussy to get working, it has some powerful capabilities, unmatched in ease of use, that make it worth the effort for some projects.

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

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

• It does nearly everything you can do in FirstGlance in Jmol, but with greater flexibility, including identifying noncovalent 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 enables 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 can be downloaded and used off-line.

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

• A clickable sequence listing shows where any residue is in the 3D structure ("Seq3D").

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

• Protein Explorer's MSA3D can 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