Abstract
Structural concepts such as the exact arrangement of a protein in three dimensions are crucial to almost every aspect of biology and chemistry, yet most of us have not been educated in three-dimensional literacy and all of us need a great deal of help in order to perceive and to communicate structural information successfully. It is in the undergraduate biochemistry course where students learn most concepts of molecular structure pertinent to living systems. We are addressing the issue of three-dimensional structural literacy by having undergraduate students construct kinemages, which are plain text scripts derived from Protein Data Bank coordinate files that can be viewed with the program MAGE. These annotated, interactive, three-dimensional illustrations are designed to develop a molecular story and allow exploration in the world of that story. In the process, students become familiar with the structure-based scientific literature and the Protein Data Bank. Our assessment to date has shown that students...
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