Alignments grow, secondary structure prediction improves
Alignments grow, secondary structure prediction improves
复制标题
DOI：
10.1002/prot.10029
复制
发表时间：
2002-02-01
影响因子：
2.9
通讯作者：
Rost, B
中科院分区：
文献类型：
--
作者：
Przybylski, D;Rost, B
使用序列比对的信息显着提高蛋白质二级结构的预测。通常情况下，更发散的配置文件产生更好的预测。最近，不同的研究小组已经表明，通过使用PSI-BLAST配置文件开发新的预测方法，可以显着提高准确性。在这里，我们专注于各种对齐策略对两个8岁的PHD方法的影响。以下结果引人注目。(i)使用成对比对的PHD预测约72%的所有残基正确地处于三种状态之一：螺旋、链和其他。使用更大的数据库和PSI-BLAST将准确率提高到75%。(ii)超过60%的改进来自于当前序列数据库的增长;约20%来自于比对程序（替换矩阵、阈值和空位罚分）的详细变化。另外20%的改进来自于仔细使用迭代PSI-BLAST搜索。(iii)有趣的是，当我们试图通过动态编程（MaxHom和ClustalW）来细化比对时，我们未能进一步提高预测准确度。(iv)通过家庭增长实现的改善似乎在某个时候达到饱和。然而，大多数家庭还没有达到这种饱和。因此，我们预计预测准确性将随着数据库的增长而继续提高。蛋白质2002;46：197-205. (C)2001 Wiley-Liss，Inc.
Using information from sequence alignments significantly improves protein secondary structure prediction. Typically, more divergent profiles yield better predictions. Recently, various groups have shown that accuracy can be improved significantly by using PSI-BLAST profiles to develop new prediction methods. Here, we focused on the influences of various alignment strategies on two 8-year-old PHD methods. The following results stood out. (i) PHD using pairwise alignments predicts about 72% of all residues correctly in one of the three states: helix, strand, and other. Using larger databases and PSI-BLAST raised accuracy to 75%. (ii) More than 60% of the improvement originated from the growth of current sequence databases; about 20% resulted from detailed changes in the alignment procedure (substitution matrix, thresholds, and gap penalties). Another 20% of the improvement resulted from carefully using iterated PSI-BLAST searches. (iii) It is of interest that we failed to improve prediction accuracy further when attempting to refine the alignment by dynamic programming (MaxHom and ClustalW). (iv) Improvement through family growth appears to saturate at some point. However, most families have not reached this saturation. Hence, we anticipate that prediction accuracy will continue to rise with database growth. Proteins 2002;46:197-205. (C) 2001 Wiley-Liss, Inc.