Date: 10 Sep 2009
From: jyrki@diku.dk
Subject: Thesis defence on protein interactions

Oral defence of M.Sc. thesis: Searching for similar binding sites

Defender: Anders Thøgersen
Censor: Christian Storm Pedersen
Supervisor: Jyrki Katajainen 

Time: 17 September 2009 at 11.00–12.00
Place: N026

The defence will be held in Danish.

Abstract

In protein research it is often important to determine with which
other proteins an interaction may occur. This can help in definition
of biological role of the protein, such as inhibition or enhancement
of particular functions.  The criterion that makes an interaction
possible is that the two proteins contain binding sites that
structurally and chemically allow the interaction to take place.

In this work a method is developed to allow the deduction of possible
new protein interactions by looking at the set of protein interactions
that are already known.

A framework has been created for experimenting with superimposition of
protein binding sites. The central methods employed are Particle Swarm
Optimization and Iterative Closest Point. Because the same protein
binding site may have variations across protein families, the removal
of outliers, i.e. atoms that should be discarded to achieve a good
superimposition of the binding site core, has been a central theme of
this work.

The developed methodology is calibrated on representative data and the
quality of superimpositions made is compared with MultiBind, an
existing program for solving this problem that uses a fundamentally
different approach.

Good superimpositions are achieved with geometrically similar
structures, but biologically significant results are obtained less
frequently. However, some experiments indicate that there is room for
significantly improving performance on biologically significant
results.

The thesis is available online: 
http://www.diku.dk/~jyrki/PE-lab/Anders/

PE-lab's home page: http://www.diku.dk/~jyrki/PE-lab/