Visualizing protein structure and function with Presentations in Protein Explorer (PiPE)

CHED 252

Karl M. Oberholser, Chemistry and Biochemistry Department, Chemistry and Biochemistry Department, Messiah College, One College Ave., Grantham, PA 17027
For about a decade a low cost approach to the study of protein and DNA structures has been to use Chime, a browser plugin. A limitation to this approach is that self-exploration of the structure beyond the descriptions provided by the scripted buttons is not convenient. Self-exploration can easily be done with the Chime based program Protein Explorer (PE), but it is not possible to supplement the self-exploration. The development of PiPE (copyright by Eric Martz, University of Massachusetts) overcomes these limitations. In the Presentation version of PE the PDB file contains tutorial material as well as the structural data. The structural elements that permit the placement of the tutorial material and Chime scripts in the PDB file will be examined, and the PiPE approach to studying protein structure will be illustrated using myohemerytherin and complex III of the mitochondrial respiratory chain.