Protein Explorer
From Proteopedia
(adding content) |
(adding content) |
||
| Line 1: | Line 1: | ||
| - | Protein Explorer ([http://proteinexplorer.org ProteinExplorer.Org]) is a free macromolecular visualization software package, written largely by [[User:Eric Martz|Eric Martz]] from 1998-2006, that works in the Firefox web browser. Protein Explorer utilizes the [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime] browser plugin (which does the interactive molecular rendering, much as the Jmol applet does in Proteopedia). Although free, Chime is not open-source, and has had very little development in recent years. There is no Chime available for Mac OS X, and even on Windows, getting Chime to work can occasionally be problematic. Protein Explorer works fully only in the [http://getfirefox.com 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. | + | Protein Explorer ([http://proteinexplorer.org ProteinExplorer.Org]) is a free macromolecular visualization software package, written largely by [[User:Eric Martz|Eric Martz]] from 1998-2006, that works in the Firefox web browser. It was designed for students and educators, but because of its power and ease of use, has also been 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 utilizes the [http://www.umass.edu/microbio/chime/abtchime.htm MDL Chime] browser plugin (which does the interactive molecular rendering, much as the Jmol applet does in Proteopedia). Although free, Chime is not open-source, and has had very little development in recent years. There is no Chime available for Mac OS X, and even on Windows, getting Chime to work can occasionally be problematic. Protein Explorer works fully only in the [http://getfirefox.com 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. | ||
Protein Explorer could be re-designed to use open-source [http://jmol.org Jmol], but this is a large undertaking. [http://www.stolaf.edu/people/hansonr/ Bob Hanson] (the major developer of Jmol in recent years) has begun this re-design, but in October 2008, his Jmol version of Protein Explorer is far from being fully operational. | Protein Explorer could be re-designed to use open-source [http://jmol.org Jmol], but this is a large undertaking. [http://www.stolaf.edu/people/hansonr/ Bob Hanson] (the major developer of Jmol in recent years) has begun this re-design, but in October 2008, his Jmol version of Protein Explorer is far from being fully operational. | ||
Revision as of 18:08, 18 October 2008
Protein Explorer (ProteinExplorer.Org) is a free macromolecular visualization software package, written largely by Eric Martz from 1998-2006, that works in the Firefox web browser. It was designed for students and educators, but because of its power and ease of use, has also been 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 utilizes the MDL Chime browser plugin (which does the interactive molecular rendering, much as the Jmol applet does in Proteopedia). Although free, Chime is not open-source, and has had very little development in recent years. There is no Chime available for Mac OS X, and even on Windows, getting Chime to work can occasionally be 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.
Protein Explorer could be re-designed to use open-source Jmol, but this is a large undertaking. Bob Hanson (the major developer of Jmol in recent years) has begun this re-design, but in October 2008, his Jmol version of Protein Explorer is far from being fully operational.
Although Protein Explorer 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.
- 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 assistance. This includes an extensive [Help/Index/Glossary].
- 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.
- 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 does a superior job of mapping evolutionary conservation onto a 3D structure, it requires a minimum of five sequences.
