Comparisons of Protein Structure Alignment Methods: Rigid and Flexible, Sequential and Non-Sequential

We try to evaluate the sequential and non-sequential and flexible structural alignment methods on SCOP 1.71. Firstly, we compare the flexible method with rigid methods and compare the sequence order dependent methods with sequence order independent methods by two typical cases. Secondly, the performances of the above methods are evaluated using ten protein pairs which are considered as "hard to detect" similarities. Thirdly, we evaluate the methods by comparing the ROC curves based on their native score and geometric measure Qscore. Then we compare the methods directly using geometric match measure Qscore, which also allows the creation of a 'Best- of-All' method. The main conclusions are: (1) we find that the best alignments found by sequential methods are more consistent with the SCOP classification; (2) we show that ROC curves are of limited value and that their ranking of the methods is not consistent with the ranking implied by the quality of the alignments the methods find; (3) we also find that the alignments of flexible method and non-sequential methods are better than the corresponding alignments of rigid sequential method from the viewpoint of geometric superposition, and flexible method and non-sequential methods can find more cross-fold similarities.