Modeling and Manipulating Biomolecular Interactions

This half of the course is taught by Prof. Ernest Fraenkel. This section contains lecture notes, reading material, and suggested study problems. There is also an associated protein design project.


Diverse problems ranging from fundamental questions of molecular biology to drug development can be analyzed in terms of the interactions between specific biomolecules, including protein-DNA and kinase-substrate interactions. Techniques for modifying these interactions are an essential part of the biological engineer's toolkit. This section of 20.320 will focus on methods for modeling and manipulating biomolecular interactions. By the end of this unit, you will know how to analyze biological networks and to re-engineer protein-protein and protein-drug complexes to make more potent biological agents.

Lecture Notes

These are Prof. Ernest Fraenkel's lecture notes.

Teaching assistants Daniel Martin-Alarcon and Allison Claas took these lecture notes during class.

Reading Material (Optional)

Buy at Amazon Scheeff, Eric D., and J. Lynn Fink. "Fundamentals of Protein Structure." In Structural Bioinformatics. Edited by Philip E. Bourne, and Helge Weissig. Wiley-Liss, 2003, pp. 15–39. ISBN: 9780471201991. [Preview with Google Books]

Buy at Amazon Grinstead, Charles M., and J. Laurie Snell, eds. This resource may not render correctly in a screen reader.Introduction to Probability (PDF - 3.06MB). American Mathematical Society, 1997. ISBN: 9780821807491. [Preview with Google Books]

Woolf, Peter, Burge Christopher, et al. Statistics and Probability Primer for Computational Biologists (PDF). 2004. (Courtesy of the authors. Used with permission.)