Reliability measures for membrane protein topology prediction algorithms
Reliability measures for membrane protein topology prediction algorithms
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DOI：
10.1016/s0022-2836(03)00182-7
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发表时间：
2003-03-28
影响因子：
5.6
通讯作者：
von Heijne, G
中科院分区：
文献类型：
--
作者：
Melén, K;Krogh, A;von Heijne, G
我们为五种广泛使用的膜蛋白拓扑预测方法开发了可靠性评分，并将其应用于由实验确定拓扑的 92 种细菌质膜蛋白的测试集，以及三个完全测序的基因组（大肠杆菌、酿酒酵母和秀丽隐杆线虫）中所有预测的螺旋束膜蛋白。我们表明，可靠性分数对于 TMHMM 和 MEMSAT 方法效果很好，并且它们允许估计任何蛋白质的预测拓扑正确的概率。我们进一步表明，与全基因组数据集相比，可用的测试集偏向于高分蛋白质，并提供了 TMHMM 在三个基因组中的预期预测准确性的估计。最后，我们表明，当可获得有限的实验信息（例如蛋白质 C 末端的进/出位置）时，TMHMM 的性能要好得多，并估计通过这种方式可以将全基因组预测的总体准确性提高至少 10 个百分点。 (C) 2003 Elsevier Science Ltd. 保留所有权利。
We have developed reliability scores for five widely used membrane protein topology prediction methods, and have applied them both on a test set of 92 bacterial plasma membrane proteins with experimentally determined topologies and on all predicted helix bundle membrane proteins in three fully sequenced genomes: Escherichia coli, Saccharomyces cerevisiae and Caenorhabditis elegans. We show that the reliability scores work well for the TMHMM and MEMSAT methods, and that they allow the probability that the predicted topology is correct to be estimated for any protein. We further show that the available test set is biased towards high-scoring proteins when compared to the genome-wide data sets, and provide estimates for the expected prediction accuracy of TMHMM across the three genomes. Finally, we show that the performance of TMHMM is considerably better when limited experimental information (such as the in/out location of a protein's C terminus) is available, and estimate that at least ten percentage points in overall accuracy in whole-genome predictions can be gained in this way. (C) 2003 Elsevier Science Ltd. All rights reserved.