Comparisons of protein structure alignment methods: rigid and flezible, 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 Bestof-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.
rigid alignment flezible alignment sequence order independent ROC curves geometric similarity
Junping Xiang Maolin Hu
Key Laboratory of Intelligent Computing & Signal Processing, Ministry of Education School of Mathematics and Computational Science Anhui University Hefei, Anhui, China
国际会议
上海
英文
21-24
2008-05-16（万方平台首次上网日期，不代表论文的发表时间）