Speaker: Dr. Silvia Crivelli
         Lawrence Berkeley National Laboratory

Title:
The Protein Structure Prediction Problem

Abstract:

Proteins are the building blocks of cells. They are composed of a
string of amino acids called the primary structure. The primary
structure of a protein and its aqueous environment give rise to forces
that guide the formation of the tertiary structure (three-dimensional
shape) that in turn determines the protein's functionality. Predicting
this tertiary structure from its primary sequence is one of the
greatest challenges in modern science.

Mathematically, the problem can be formulated as a global minimization
problem, as it is assumed that the tertiary structure occurs at the
global minimum of the free energy function of the amino acid
sequence. However, finding the global minimum is a challenging task
because the energy function of a realistic-sized protein has thousands
of parameters and a large number of low-lying local
minima. 

Computationally, the problem can be represented as a search through a
huge tree of possible solutions where the root of the tree corresponds
to the primary sequence and the leaves to the local minima.  The
problem is challenging also from this point of view and requires the
efficient use of parallel computers. Scientist have estimated that
solving the structure prediction problem by traversing the entire tree
would take 10^27 years for an average-sized protein on a single
computer.  In this talk, I will describe the method that we have
developed for tackling this problem and discuss some outstanding
issues involved in this truly multidisciplinary research.