Evaluation of protein dihedral angle prediction methods.
Evaluation of protein dihedral angle prediction methods.
复制标题
DOI：
10.1371/journal.pone.0105667
复制
发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Raghava GP
中科院分区：
文献类型：
--
作者：
Singh H;Singh S;Raghava GP
从氨基酸序列预测蛋白质的三级结构是生物信息学领域的主要挑战之一。层次分析法是预测蛋白质三级结构的有说服力的技术之一，特别是在缺乏同源蛋白质结构的情况下。在分层方法中，预测了中间态如二级结构、二面角、Cα-Cα距离界等。这些中间状态用于抑制蛋白质骨架并帮助其正确折叠。近年来，人们发展了几种预测蛋白质二面角的方法，但很难确定哪种方法比其他方法更好。在本研究中，我们对二面体预测方法ANGLOR和SPINE X在各种数据集（包括独立数据集）上的性能进行了基准测试。没有对TANGLE二面体预测方法进行基准测试（由于其独立的不可用性），并且仅在TANGLE报告其结果的ANGLOR数据集上与SPINE X和ANGLOR进行比较。观察到SPINE X比ANGLOR和TANGLE表现更好，特别是在预测甘氨酸和脯氨酸残基的二面角时。分析表明，角度偏移是SPINE X性能更好的主要原因。我们进一步评估了独立ccPDB30数据集上的方法性能，并观察到SPINE X的性能优于ANGLOR。
Tertiary structure prediction of a protein from its amino acid sequence is one of the major challenges in the field of bioinformatics. Hierarchical approach is one of the persuasive techniques used for predicting protein tertiary structure, especially in the absence of homologous protein structures. In hierarchical approach, intermediate states are predicted like secondary structure, dihedral angles, Cα-Cα distance bounds, etc. These intermediate states are used to restraint the protein backbone and assist its correct folding. In the recent years, several methods have been developed for predicting dihedral angles of a protein, but it is difficult to conclude which method is better than others. In this study, we benchmarked the performance of dihedral prediction methods ANGLOR and SPINE X on various datasets, including independent datasets. TANGLE dihedral prediction method was not benchmarked (due to unavailability of its standalone) and was compared with SPINE X and ANGLOR on only ANGLOR dataset on which TANGLE has reported its results. It was observed that SPINE X performed better than ANGLOR and TANGLE, especially in case of prediction of dihedral angles of glycine and proline residues. The analysis suggested that angle shifting was the foremost reason of better performance of SPINE X. We further evaluated the performance of the methods on independent ccPDB30 dataset and observed that SPINE X performed better than ANGLOR.
登录
查看更多内容
影响因子：
3
作者：
Faraggi, Eshel;Zhang, Tuo;Yang, Yuedong;Kurgan, Lukasz;Zhou, Yaoqi
通讯作者：
Zhou, Yaoqi
影响因子：
14.9
作者：
Cole C;Barber JD;Barton GJ
通讯作者：
Barton GJ
影响因子：
5.8
作者：
Kaur, H;Raghava, GPS
通讯作者：
Raghava, GPS
影响因子：
8
作者：
Kaur, H;Raghava, GPS
通讯作者：
Raghava, GPS
影响因子：
2.9
作者：
Dor, Ofer;Zhou, Yaoqi
通讯作者：
Zhou, Yaoqi