ZPRED:: Predicting the distance to the membrane center for residues in α-helical membrane proteins
ZPRED:: Predicting the distance to the membrane center for residues in α-helical membrane proteins
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DOI：
10.1093/bioinformatics/btl206
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发表时间：
2006-07-01
期刊：
影响因子：
5.8
通讯作者：
Elofsson, Arne
中科院分区：
文献类型：
--
作者：
Granseth, Erik;Viklund, Hakan;Elofsson, Arne
动机：预测方法对于膜蛋白是非常重要的，因为实验信息比球状蛋白更难获得。随着越来越多的膜蛋白结构被解决，很明显，拓扑信息只能提供一个简化的膜蛋白的图片。在这里，我们描述了一个新的挑战，预测a-螺旋膜蛋白：来预测残基和膜中心之间的距离，我们将其定义为Z坐标。尽管描述膜蛋白拓扑结构的传统方法是有用的，它是有利的，有一个措施，是基于一个更“物理”的属性，如Z坐标，因为它隐含地包含有关的信息，再入螺旋，界面螺旋，跨膜螺旋和环lengths.Results的倾斜：我们表明，Z坐标可以预测使用人工神经网络，隐马尔可夫模型或两者的组合。最好的方法ZPRED使用隐马尔可夫模型和神经网络的输出。ZPRED的平均误差为2.55埃，并且在5-25埃区域中，68.6%的残基被预测在目标Z坐标的3埃内。ZPRED还能够预测数据集中78%的环的最大突出度在3A以内。
Motivation: Prediction methods are of great importance for membrane proteins as experimental information is harder to obtain than for globular proteins. As more membrane protein structures are solved it is clear that topology information only provides a simplified picture of a membrane protein.Here, we describe a novel challenge for the prediction of a-helical membrane proteins: to predict the distance between a residue and the center of the membrane, a measure we define as the Z-coordinate.Even though the traditional way of depicting membrane protein topology is useful, it is advantageous to have a measure that is based on a more "physical" property such as the Z-coordinate, since it implicitly contains information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.Results: We show that the Z-coordinate can be predicted using either artificial neural networks, hidden Markov models or combinations of both. The best method, ZPRED, uses the output from a hidden Markov model together with a neural network. The average error of ZPRED is 2.55 angstrom and 68.6% of the residues are predicted within 3 angstrom of the target Z-coordinate in the 5-25 angstrom region. ZPRED is also able to predict the maximum protrusion of a loop to within 3A for 78% of the loops in the dataset.