Protein Explorer: Difference between revisions
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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 [http://about.merlot.org/MERLOTAwards/2003awards.html Merlot Classic Award] for Exemplary Learning Materials in Biology: "Protein Explorer has revolutionized the teaching of biology at a molecular level.". | Protein Explorer ([http://proteinexplorer.org ProteinExplorer.Org])<ref>Protein Explorer: Easy Yet Powerful Macromolecular Visualization. Eric Martz. ''Trends in Biochemical Sciences'', '''27''' (February):107-109, 2002.</ref> 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 [http://about.merlot.org/MERLOTAwards/2003awards.html 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 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. | ||
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* 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 [[Conservation, Evolutionary|ConSurf Server]] does a superior job of mapping evolutionary conservation onto a 3D structure, it requires a minimum of five sequences. | * 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 [[Conservation, Evolutionary|ConSurf Server]] does a superior job of mapping evolutionary conservation onto a 3D structure, it requires a minimum of five sequences. | ||
==See Also== | |||
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