The exercises in this tutorial were developed at Reed College in Portland, Oregon by Arthur Glasfeld for use in an undergraduate course devoted to structural biochemistry. The main purpose of these exercises has been to introduce third and fourth year undergraduates to biomolecular structure, but another significant goal has been to acquaint the user with MidasPlus, a molecular modeling package written at the Computer Graphics Lab at UCSF, providing a gradual introduction to the functions of the software package. Hopefully any individuals who are interested in learning Midas themselves will find this a useful introduction. It is also hoped that these exercises will be useful to students to students in structural biochemisty courses.
Getting Started
These exercises have been written to be used with Midas v2.1 running on Silicon Graphics platforms. Older versions of Midas, and those running on different platforms, support virtually all of the functions that are used, but the specific commands may be different in a few places. Before getting started, the user should be familiar with Netscape, with simple UNIX commands and with a text editor such as vi or jot. It's suggested that an open UNIX shell be available for running Midas, before initiating an exercise.
The coordinate files that accompany this tutorial are all in the Brookhaven Protein Data Bank (PDB) format. For a brief description of this format, see Appendix A.
The first five exercises provide experience with an increasing number of commands and options within Midas. The remaining five are largely dependent on the skills learned in the earlier exercises, but increase the complexity of the models. Any comments on the exercises would be appreciated. Please forward them to glasfeld@reed.edu
The Exercises
1. Intermolecular Interactions in Crystalline Glycyl-L-threonine Dihydrate
2. The Ramachandran Plot
3. The N-terminus Problem
4. The Tertiary Fold of BPTI
5. Rational Drug Design Applied to the Influenza Virus
6. Papain and Its Relationship to the Serine Proteases
7. The Structural Basis of Dehydrogenase Stereospecificity
8. Functional Aspects of Modified Bases in tRNA
9. Redesigning Zinc Finger Specificity
10. Substrate Specificity in Seryl-tRNA Synthetase
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