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Peer Review

BioMolecular Explorer 3D (BME3D)

by Frieda Reichsman


Overall Numeric Rating:

4.67 stars
Content Quality: 5 stars
Effectiveness: 4.3 stars
Ease of Use: 4 stars
Reviewed: Feb 24, 2006 by Biology Editorial Board
Overview: Biomolecular Explorer 3D provides easy access to interactive 3D structures of biologically significant molecules including; Antibodies, Collagen, DNA, Hemoglobin, HIV Protease, Lactase, Lac Repressor, Lipid Bilayers, Myosin, and a nucleosome. The tutorials walk students through important aspects of protein structure, and the interactions between macromolecules.
Type of Material: Animations and interactive 3D tutorials.
Recommended Uses: In-class demonstration or out-of-class tutorial.
Technical Requirements: Molecules at the BioMolecular Explorer 3D web site are accessed using a compatible browser and MDL Chime software.
* Compatible browsers are:
1. Netscape 4.8: fully compatible with all BME3D materials, this is the most stable for tutorials.
2. Netscape 7.2, Firefox, Mozilla: minor incompatibilities.
3. Internet Explorer: compatible with only some resources.
* MDL Chime: a "plug-in" that equips certain browsers to display molecular structures. Link to download and installation instructions is provided.
Identify Major Learning Goals: Interactive molecular exploration in High School Biology courses
Target Student Population: High school Biology, but would also be good for college courses.
Prerequisite Knowledge or Skills: Basic biology and general structure of macromolecules.

Evaluation and Observation

Content Quality

Rating: 5 stars

  • Good variety of different tpyes of biological moleucles.
  • Guided tutorials work well and provide step by step instructions.
  • Excellent graphics that walk students through fairly complex structures in an easy to follow fashion.
  • Covers the main components of a cell including excellent tutorials on phoshpolipid membranes and DNA.
  • Links to background materials that help students connect the structures with biological processes.

  • Might be a bit complex for high school students to grasp

Potential Effectiveness as a Teaching Tool

Rating: 4.3 stars

  • Would be possible for teachers to write exercises based on the tutorials, but none were provided.
  • Excellent visual demonstration of complex macromolecular structures and interactions.
  • 3D visuals should work well in the cases of the tutorials.

  • Not sure the Protein Explorer links will be used by HS teachers. Tutorials seem much more useful.
  • Would be stregthened by direct ties to actual HS biology learning outcomes.
  • Some tutorials are very sparse on text and explanation, which would help students follow what is going on. This may be difficult for some students to use on their own, and would require some explanation from the teacher.
  • There weren't any exercises or questions for students to answer to see if they understood what was being taught in the tutorials.

Ease of Use for Both Students and Faculty

Rating: 4 stars

  • No broken links, tutorials loaded quickly, easy to navigate and well organized.
  • Web instructions are clearly outlined on the home page.
  • Sections are defined well.
  • Good assistance is offered for Netscape 4.8 download.
  • Tutorials run well all buttons are active.

  • The main page is easy to navigate, but once you are in the tutorial it is hard to get back to the main page. Essentially the student has to just close the window.
  • If more than one tutorial is open at once, occasionally the commands get crossed.
  • Some browser incompatabilities may make it difficult for some students or classrooms to install and use.
  • Concerns that the requirement for Netscape 4.8 might turn some off to the site.

Other Issues and Comments: Overall a good site that introduces 3D into biology for HS students.
In general I wonder if a separate basic protein structure tutorial would assist
before students are to delve into the details.
Comments from Author: The entire site is available on CD (at cost, $12) which means you can install Netscape 4.8 and Chime right from the CD. This simplifies the whole process even further, especially for teachers in schools that do not have reliable and/or high speed internet connections. No need to go online, no need to register with MDL, and the tutorials and PE are all right there on the CD.