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Peer Review

Protein Explorer

by Eric Martz


Overall Numeric Rating:

5 stars
Content Quality: 5 stars
Effectiveness: 5 stars
Ease of Use: 5 stars
Reviewed: Jan 29, 2002 by Biology Editorial Board
Overview: Protein Explorer (PE) is an interactive software package that allows the visualization of three dimensional structures of amino acids, proteins and DNA determined by NMR or crystallography. It uses an intuitive interface to the browser plug-in program Chime. PE must be run using the Netscape browser (version 4.7+, but not Netscape 6!) or MS Internet Explorer 5.5. Students have access to the high quality graphics of Chime combined with the power of RasMol to manipulate 3D structures. A major advantage over RasMol is that manipulations can be made with an easy point and click interface and don't require entering commands line by line. PE supports nearly all of the RasMol and Chime commands and offers a plethora of automated (button push) manipulations of molecules. Consequently, PE is useful to novices as well as experts. One of the most impressive of PE's many features is the contact-surfaces option. This produces spectacular views of intermolecular interactions. This feature, coupled with PE's noncovalent-bond finder, allows users to investigate weak interactions at the heart of macromolecular structure. Another advance is the multiple-sequence-alignment tool, which permits the visualization of conserved residues of homologous structures. PE can be effectively used in class, but is especially useful in student-run investigations of macromolecular structure. There are several tutorials and example molecules to help orient students with the basic operation of the program.
Type of Material: Interactive program
Technical Requirements: A web browser (Netscape or Internet Explorer 5.5), Chime 2
Target Student Population: Any level of college student.

Evaluation and Observation

Content Quality

Rating: 5 stars
Strengths: (5)(5) = (5)

? A research grade program made available for free as a web-based program. A complete suite of modeling applications.
? Linked to major databases and tutorials.
? Online instruction manual.
? Demonstration molecule easy to load.
? Interactive, powerful visualizations of macromolecular structure
? Different modes for beginning or advanced visualization
? Sets of automated commands for common rendering options
? Allows viewing of any molecule stored in the popular Protein Data Bank (PDB) format
Concerns: None

Potential Effectiveness as a Teaching Tool

Rating: 5 stars
Strengths: (5)(5) = (5)

? Easy to navigate and quick, without any defective links or bugs.
? Links on the first page allows for quick access to program and examples.
? The Protein Explorer front page has links to help users find the PDB codes (required for PE viewing) for molecules of interest
? Advanced users can use Chime scripting commands to change the rendering of the molecule
? Beginning users can use the many automated buttons to invoke pre-specified Chime scripts
Concerns: ? It is not obvious at first glance how to bring up the structure of a molecule other than the Gal4 example molecule. A link to search PDB light is available at the center of the page, you may need to direct student's attention to this link.

Ease of Use for Both Students and Faculty

Rating: 5 stars
Strengths: (5)(5) = (5)

? A good supplement to a text or used as a stand-alone module.
? Highly interactive, inquiry-based and open-ended.
? Would be possible to write questions based upon structures being viewed, as seen in "Lesson Plans" link.
? Users can quickly visualize key macromolecular features using a variety of automated buttons
? Users can change a molecule's orientation quickly and easily by clicking and dragging
? Various rendering options are easily invoked
Concerns: ? It would probably be necessary to give students detailed instructions on their first exposure to this program. A tutorial is provided.
? Provided the instructor is prepared to coach beginning students in their first encounters with PE, none