[Molvis-list] Current BAMBEd bounteous with structure

Eric Martz emartz at microbio.umass.edu
Sat Oct 29 13:30:48 EDT 2005

The current issue of Biochemistry and Molecular Biology Education  
(http://www.bambed.org/) is outstanding, and has more articles  
concerning structure than usual.

The lead article is by Todd Weaver and Scott Cooper, "Exploring  
protein function and evolution using free online bioinformatics  
tools". In the next release of Protein Explorer, under Lesson Plans  
(linked to PE's FrontDoor), I will describe it as follows:

This article describes a protein structure exercise within a  
bioinformatics course at Univ. Wisconsin-La Crosse, taught to about  
40 students twice a year. This exercise is allocated 6-8 h in class  
(computer laboratory) plus homework. The software employed is Biology  
Workbench, Protein Explorer, and ConSurf. Students are assigned an  
amino acid sequence, and asked to make predictions about functional  
motifs, secondary structure (noting differences obtaine with  
different programs), hydrophobic and transmembrane regions. Students  
are then asked to assess the accuracy of the preditions, including  
secondary structure predictions assessed with an empirical 3D  
structure in Protein Explorer. Finally, students explore conservation  
in multiple sequence alignments between orthologs and paralogs, and  
examine conserved or hypervariable patches in the 3D structure.  
Seventeen proteins are listed that work well for this exercise.  
Online materials are provided.

In the second article, Scott Cooper describes MERLOT, which has links  
to 1,300 electronic teaching resources in biology and chemistry. 20%  
of these have been peer-reviewed and rated in various categories.  

In another article, Sayan Mukherjee et al. describe "A docking  
interaction study of the effect of critical mutations in ribonuclease  
A on protein-ligand binding", using AutoDock and PyMol (freely  
available for academic use).

In yet another article, Scott E. Thompson and Duane Sears describe  
"Simplifying structure analysis projects with customizable chime- 
based templates". Duane is a pioneer in electronic structural biology  
and biochemistry education, and these are highly-developed teaching  
modules used at U. Cal. Santa Barbara. Their templates, tutorials,  
and course website are available at

Finally, Gale Rhodes, another pioneer in the field of structural  
biology education, provides a thoughtful analysis of his experiences,  
emphasizing the changing attitudes of peer-evaluation committees  
towards development of on-line educational resources, methods of  
weighting such activities vis a vis traditional publications, how he  
has documented his activities, and how his peers have responded. His  
popular website begins at http://www.usm.maine.edu/~rhodes

Many other excellent articles, commentaries, websites of note, and a  
poem complete this outstanding issue. Judy and Don Voet, as editors  
in chief, are to be congratulated for their achievements in building  
the quality and quantity of BAMBEd's contents!


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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz

Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
Biochem Structure Tutorials http://MolviZ.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
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