Protein Threading Based on Multiple Protein Structure Alignment
Tatsuya Akutsu (email@example.com)
Kim Lan Sim (firstname.lastname@example.org)
Human Genome Center, Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
Protein threading, a method employed in protein three-dimensional (3D)
structure prediction was only proposed in the early 1990's although
predicting protein 3D structure from its given amino acid sequence
has been around since 1970's.
Here we describe a protein threading method/system that
we have developed based on multiple protein structure alignment.
In order to compute multiple structure alignments,
we developed a similar structure search program on massive parallel computers
and a program for constructing a multiple structure alignment from
pairwise structure alignments,
where the latter is based on the center star method for sequence alignment.
A simple dynamic-programming based algorithm
which uses a profile matrix obtained from the result of multiple
structure alignment was also developed to compute a threading
(i.e., an alignment between a target sequence and a known structure).
Using this system, we participated in the threading category (category AL) of
CASP3 (Third Community Wide Experiment on the Critical Assessment of Techniques
for Protein Structure Prediction).
The results are discussed.
Japanese Society for Bioinformatics