Speaker: Bonnie Berger
Title: Mathematical Challenges in Protein Motif Recognition.
Affiliation: Massachussets Institute of Technology.
Date: Friday, November 19.
Place and Time: Room 101 - Love Building, 3:30-4:30 pm.
Refreshments: Room 204 - Love Building, 3:00 pm.
Host: DeWitt Sumners.

Abstract. One of the most important and challenging problems in computational biology is that of predicting the three-dimensional structure or shape of a protein from its amino acid sequence. As a first step to tackling this problem, many researchers have focused on the structural motif recognition problem: given a known local three- dimensional structure, or motif, determine whether this motif occurs in a given amino acid sequence. In this talk, I will present algorithms that use probabilistic techniques to improve existing methods for recognizing protein structural motifs. These algorithms are particularly effective at eliminating false positives found by previous methods without introducing false negatives. Our programs have been useful in identifying coiled-coil-like motifs in the envelope proteins of many viruses, such as the influenza virus, Moloney murine leukemia virus, HIV, SIV, and visna virus, whose structures have since been solved. This in turn has led to antiviral drug discovery by the Peter Kim lab at MIT.