Samo

                a protein Structure Alignment tool
             based on Multiple Objective optimization

                         [Version 0.01.004]

                           June 3, 2005

              http://zhangorup.aporc.org/bioinfo/samo/


AUTHORS
=======

Ling-Yun Wu     aloft@ctex.org
Yong Wang       ywang@ctex.org


METHOD
======

Protein structure alignment is one of the important computational problems
in molecular biology and plays a key role in protein structure prediction,
fold family classification, motif finding, phylogenetic tree reconstruction
and protein docking.

We propose a novel method (SAMO) for solving the structure alignment problem in
an accurate manner at the amino acid level, based on a decomposition
technique. SAMO is able to align protein structures, reveal divergent evolution, detect circular permutations and identify structural motifs.  

We define the structure alignment as a multi-objective optimization problem
with both integer and continuous variables, i.e., maximizing the matching
number of proteins and minimizing their root mean square distance.

By exploiting the special structure of the protein alignment, the original
problem is decomposed into two subproblems: one linear programming
subproblem (LPS) for the protein matching and one weighted least square
subproblem (LSS) for coordinate transformation.

A very efficient algorithm is developed for optimizing LPS and LSS. By 
controling a single distance-related parameter, theoretically we can obtain
a variety of optimal alignments corresponding to different optimal matching
patterns, i.e., from a global alignment with a large matching portion to
a local alignment with a small matching portion.


REFERENCE
=========

Chen L, Wu LY, Wang R, Wang Y, Zhang S, Zhang XS: Revealing Divergent Evolution, Identifying Circular Permutations and Detecting Active-Sites by Protein Structure Comparison. In submission. 

SOFTWARE
========

This version of the program is in very preliminary stage and provided just
for testing purpose. The program is still under development.