A HMM-based method to predict the transmembrane regions of β-barrel membrane proteins
A HMM-based method to predict the transmembrane regions of β-barrel membrane proteins
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DOI：
10.1016/s0097-8485(02)00051-7
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发表时间：
2003-02-01
影响因子：
3.1
通讯作者：
Li, YX
中科院分区：
文献类型：
--
作者：
Liu, Q;Zhu, YS;Li, YX
开发了一种新方法来建模和预测 β-桶膜蛋白的跨膜区域。它基于隐马尔可夫模型 (HMM)，其结构遵循这些蛋白质的构建原则。 HMM 在一组非冗余的 11 种 β-桶膜蛋白上进行训练和测试，这些蛋白迄今为止已通过折刀程序达到原子分辨率。结果，该方法正确定位了 172 条跨膜 β 链中的 97%。在 11 种蛋白质中，正确预测了 10 种蛋白质的桶大小和 7 种蛋白质的整体拓扑。此外，它还成功地分配了两种新的 β-桶膜蛋白的整个拓扑结构，这两种蛋白与 11 种蛋白没有显着的序列同源性。论文还提出了线粒体外膜 β 桶结构的两个候选者的预测拓扑。 (C) 2002 Elsevier Science Ltd. 保留所有权利。
A novel method is developed to model and predict the transmembrane regions of beta-barrel membrane proteins. it is based on a Hidden Markov model (HMM) with architecture obeying those proteins' construction principles. The HMM is trained and tested on a non-redundant set of 11 beta-barrel membrane proteins known to date at atomic resolution with a jack-knife procedure. As a result, the method correctly locates 97% of 172 transmembrane beta-strands. Out of the 11 proteins, the barrel size for ten proteins and the overall topology for seven proteins are correctly predicted. Additionally, it successfully assigns the entire topology for two new beta-barrel membrane proteins that have no significant sequence homology to the 11 proteins. Predicted topology for two candidates for beta-barrel structure of the outer mitochondrial membrane is also presented in the paper. (C) 2002 Elsevier Science Ltd. All rights reserved.