Methods for Structural Alignment and their Application to Linking Protein Folds
Structural Alignment complements Sequence Alignment in that it compares protein three-dimensional structures
rather than their one-dimensional sequences. It is a technique that is essential for studying the connections
between proteins that result from evolution as sequence alignment is much less powerful than structural
alignment. In other words structural alignment can detect significant similarities between proteins that are
much more dissimilar than can be detected by sequence alignment. This greater sensitivity comes at a price:
the powerful, O(n2) method of dynamic programming can be applied to sequence alignment, whereas structural
alignment is at least O(n8). As a result there is just one basic method to compare sequences (albeit with many
modifications which make the method faster), there are at least 50 methods to compare structures. We developed
one of the first such methods, Structal, and have recently compared its performance to some of the other
powerful and popular methods. This tutorial will describe the basic principles of structural alignment, explain
its complexity, compare the performance of different methods and show how structural alignment aids automatic
classification of protein folds.
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Kolodny R., Koehl P. and M. Levitt. (2005). Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J. Mol. Biol . 346 : 1173-1188.