UniServe€Science News: Newsletter of the Science Software Clearinghouse Vol. 2, November 1995

IMDAD Viewer

for Stryer's Biochemistry (4th Edition)

Gareth Denyer is a Lecturer in Biochemistry at the University of Sydney

It is almost impossible for most students to visualise, with the mind's-eye, the complex three-dimensional structure of biological macromolecules. Furthermore, no amount of static textbook pictures can allow the student to actually explore macromolecular structure. IMDAD VIEWER, which accompanies the 4th Edition of Stryer's Biochemistry, allows 35 selected computer-generated, macro-molecular models to be viewed in three-dimensions, from any angle, and along any axis.

With the Power Macintosh version, the molecular rotations are seamless with even the perspective and shadings being rapidly updated as the model tumbles. The program allows different sections of the molecules to be highlighted and, also, for models to be depicted in space filling mode. This is useful: otherwise it's like trying to visualise the fine features of an animal from its skeleton! A feel for the enormous complexity of protein tertiary structure is also provided by other options which bring the amino acid side chains into view. The rotation of each macromolecule is, however, severely slowed by viewing anything other than a ball and stick model, particularly on the pre-Power Mac versions. It is possible to magnify and reduce the molecule using a zoom tool, but magnification, too, slows down rotations. A great feature for teachers is that screen images can be captured as PICT files -- no longer will it be necessary to scour all the textbooks to find that seminal view!

The power of the software is best illustrated by the models of the leucine zipper. Trying to explain to students how the peptides in this protein twist around each other and then intercalate a 3-D DNA-double helix is exceptionally difficult. The computer rotations not only allow each facet of the molecular contacts to be explored, but also for the key residues in each coupling to be viewed in isolation from the other interactions.

My most serious criticism is that far too much room is given to reproducing pictures from the accompanying textbook. It is unlikely that students need 3-D rotations to understand the structure-function relationships for most of the molecules included, e.g., glycogen phosphorylase. Illustration of simple, classic structures, such as collagen and keratin, would be more helpful. In some cases the graphics are not used to good effect: e.g., rotating and exploring the model of the antibody-antigen complex does not reveal how these two molecules interact

At no stage does the program help student appreciate why proteins fold the way they do. The lack of fundamental secondary structures such as alpha-helices and beta-sheets are glaring omissions. It seems almost pointless to depict large macromolecules unless the user understands these basic structures. In this respect, the software is a clearly behind Kinemages, another 3-D macromolecular viewing program which accompanies a competing textbook!

It is unlikely that students will purchase the program, but the facility to save the screen image, and the increasing availability of computer-projection facilities, means that this software may be very attractive to lecturers in macromolecular structure. It certainly beats trying to draw proteins with a blackboard and chalk!

Gareth Denyer


Platform: Macintosh, PowerMacintosh, Windows
Cost: Free if text is adopted, $22.95 for students
Macintosh: System 6+, 5 MB RAM, 2 MB free hard disc space
PC: Windows 3.1+, 386DX with math co-processor or 486DX or Pentium, 8 MB RAM.
Author: Michael Levitt
Supplier: Jacaranda Wiley Ltd, PO Box 1226, Milton Qld 4064 Tel: (07) 3 859 9755

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