Bioinformatics Algorithms: Techniques and Applications

DYNAMIC PROGRAMMING ALGORITHMS FOR PROTEIN STRUCTURE COMPARISON 23
FIGURE 2.6 Structure alignment. (a) An example of structure alignment; (b) Definition of
aligned fragment pair (AFP); (c) Pairwise structure alignment by chaining aligned fragment
pairs; (d) Multiple structure alignment by partial order alignment.
2.4.1 Structure-Based Sequence Alignment
A simple strategy for protein structure comparison is to represent a protein structure as
a sequence of characters (1D representation) that describe the structural environment
of a residue in a protein (called 3D environment). Then protein structure comparison
can be essentially transformed as a general sequence alignment problem, and conventional
dynamic programming algorithms for sequence alignment can be used directly
for solving these problems, just with different sets of characters and with a different
scoring function. This type of structure alignment could be as fast as sequence alignment.
Though they may not be as accurate as those methods that consider real 3D
structural information, but at least can serve as a quick filter to speed up the structural
similarity search, which is often much more time consuming. Main development
along this direction includes to find a better 1D representation of 3D structures so that
spatial information can be retained as much as possible.
2.4.2 Comparison of Distance Matrix: Double Dynamic Programming
Double dynamic programming algorithm was one of the early programs for structure
comparison [65]. It was named because dynamic programming procedure is applied
at two different levels: at a low level to get the best score (describing the similarity