Bio-Organic Reaction Animations (BioORA) can be used as a teaching tool for bio-inorganic courses. BioORA illustrates large biomolecules obtained from crystal structures in the Protein Data Bank using Jmol. The student can manipulate this structure, which is shown on the right-hand side of the screen of BioORA. On the left-hand side of the screen a stripped-down view of the binding site is shown. This stripped down representation can also be manipulated and has three viewing options: ball and stick, tube, and space-filling. The software helps students visualize the three-dimensional aspects of enzyme chemistry. There are more than 25 animations and several of them have coordinating metals involved in the reaction mechanisms that are illustrated.
BioORA is a visualization program for biochemistry that will focus on molecular events. The natural tendency has been to substitute acronyms for the biomacromolecules. This is an understandable result in light of the size of the relevant structures. However, we have shown that computer imaging technology is sufficiently advanced now to handle animations of the actual molecules involved in the biochemical pathways. This type of multimedia presentation can provide students with three-dimensional representations of the biomolecules and three-dimensional animations of binding and enzyme catalyzed reactions.
Our goal is to bring the molecular aspects of biochemistry to the forefront. The chemistry for the bio-organic processes is documented and the 3D visualization software is now accessible. There is a need for more accurate molecular representation and we are eager to provide it. We expect that students, regardless of their major, will benefit from this teaching tool. We hope that it will improve student appreciation of the organic chemistry that occurs in biological systems.