Guest Speaker

Geometric Techniques For Protein Structure Analysis

Yusu Wang
Duke University

Thurs., Feb. 26th
3:30pm; 480 Dreese Labs
All interested parties are invited.
Refreshments will be served immediately preceding the talk.

Abstract:
In this talk, we will discuss some approaches towards shape analysis
and matching by combining both geometry and topology of the underlying
shape. We will mainly focus on applications from structural biology --
one of the main challenges in molecular biology in the post-genomic
era is the determination and exploitation of the three-dimensional
protein structure and function. To attack the key problems involved,
such as protein folding and docking, geometry and topology become
important tools. Despite their essential roles, geometric and
topological methods are relatively uncommon in computational biology,
partly due to remaining modeling and algorithmic issues. In this talk,
we will present some of our current effort in closing this gap.
In particular, we will describe two shape characterizations, and their
applications to molecular shape classification and matching.

(i) To characterize protein backbones, we study the "writhing
number" of a space curve, and develope efficient algorithms to
compute it. The writhing number of a curve measures how much
the curve coils around itself, and was originally used to
characterize the supercoiling phenomenon of double stranded DNA.

(ii) To characterize a molecular surface, we design a continuous
"elevation function" on the surface. The function is invariant
under rigid motions and provides a description of location,
direction and size of shape features such as protrusions and
pockets of a molecular surface. Such features are useful in
attacking the protein-docking problem, which from a geometric
perspective, can be formulated as the problem of searching for
configurations with maximum complementarity between two molecular
surfaces. Some preliminary results in this direction will be
presented.

Host:Tamal Dey