Instructors: Jane and David Richardson

This is a seminar/lab course in the 3D structure of macromolecules, primarily using computer graphics. Class time is Thursday afternoons in room 437 Nanaline Duke Bldg., for discussion, reports, working/playing with brass or plastic molecular models, etc. For the first half of the course each week there is a lab exercise, done singly or in pairs at times, places, and computers of the student's choosing, primarily working with kinemages and the KiNG (or Mage) display program on Linux, Unix, Mac or Windows, or directly on the Web. Assistance with the exercises or software is available from the TA for BCH222, or in the Richardson lab (211 Nanaline Duke) after class or on other afternoons. For the second half of the course each student will do an individual project, giving a brief progress report in class every other week and a final presentation at the end in kinemage form.

The course web site contains the exercises, kinemage files, and other information. The site can be reached directly at http://kinemage.biochem.duke.edu/teaching/bch222/ and it is also linked from the Biochemistry Department's web site under the "Programs/Course of study/courses" section.

General references for course

J. S. Richardson (1981) "The Anatomy and Taxonomy of Protein Structure", Adv. Prot. Chem. 34, pp. 167-339.

This document is in the process on being annotated/updated in an online version.

C.I. Branden and J. Tooze (1999) Introduction to Protein Structure, Second Edition, Garland Publishing.

(Should be available in either the Duke or the Medical Center bookstores.) There is a "kinemage supplement" to each chapter of this text. We will use several of these kin files in the class exercises, and they are available from the kinemage web site, use the link at left.

J. S. Richardson & D. C. Richardson (1989) "Principles and Patterns of Protein Conformation" in Prediction of Protein Structure and Principles of Protein Conformation, ed. G. D. Fasman, Plenum Press, pp. 1-98.

This is available in the Richardson lab, if you can't find it elsewhere. A few sections will be handed out.

Journal articles relevant to specific lessons will also be handed out during the course.

The initial lessons will be organized around the annotated Anatomy & Taxonomy - for the first week, read the Background section (I.) of the on-line version. All three references constitute a background resource in which to look things up over the entire semester. The amount you make use of them will depend on your type and level of background. For the first week, use them to check out your familiarity with the terms and concepts (for example, amino-acid structures or cis peptides).