Debe Derek A, Danzer Joseph F, Goddard William A, Poleksic Aleksandar
Eidogen-Sertanty Inc., San Diego, California 92121, USA.
Proteins. 2006 Sep 1;64(4):960-7. doi: 10.1002/prot.21049.
STRUCTFAST is a novel profile-profile alignment algorithm capable of detecting weak similarities between protein sequences. The increased sensitivity and accuracy of the STRUCTFAST method are achieved through several unique features. First, the algorithm utilizes a novel dynamic programming engine capable of incorporating important information from a structural family directly into the alignment process. Second, the algorithm employs a rigorous analytical formula for profile-profile scoring to overcome the limitations of ad hoc scoring functions that require adjustable parameter training. Third, the algorithm employs Convergent Island Statistics (CIS) to compute the statistical significance of alignment scores independently for each pair of sequences. STRUCTFAST routinely produces alignments that meet or exceed the quality obtained by an expert human homology modeler, as evidenced by its performance in the latest CAFASP4 and CASP6 blind prediction benchmark experiments.
STRUCTFAST是一种新型的轮廓-轮廓比对算法，能够检测蛋白质序列之间的微弱相似性。STRUCTFAST方法通过几个独特的特性实现了更高的灵敏度和准确性。首先，该算法利用了一种新型动态规划引擎，能够将来自结构家族的重要信息直接纳入比对过程。其次，该算法采用了严格的轮廓-轮廓评分解析公式，以克服需要可调参数训练的临时评分函数的局限性。第三，该算法采用收敛岛统计（CIS）为每对序列独立计算比对分数的统计显著性。STRUCTFAST通常能产生达到或超过专业人类同源建模者所获得质量的比对结果，其在最新的CAFASP4和CASP6盲预测基准实验中的表现证明了这一点。
