PRED-TMBB:: a web server for predicting the topology of β-barrel outer membrane proteins
PRED-TMBB:: a web server for predicting the topology of β-barrel outer membrane proteins
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DOI：
10.1093/nar/gkh417
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Hamodrakas, SJ
中科院分区：
文献类型：
--
作者：
Bagos, PG;Liakopoulos, TD;Hamodrakas, SJ
β桶外膜蛋白构成了两个已知的结构类膜蛋白之一。尽管有几种基于网络螺旋膜蛋白的基于Web的预测因子，但目前尚无针对β-桶膜蛋白的免费预测方法，至少具有可接受的准确性。我们在这里提出了Web服务器（pred-tmbb，http://bioinformatics.biol.uoa.gr/pred-tmbb），能够预测跨膜链和β-桶式β-桶外膜蛋白的拓扑和拓扑的拓扑。 。该方法基于一个隐藏的马尔可夫模型，该模型根据条件最大似然标准训练。对该模型进行了重新训练，并且训练集现在包括16个非同源外膜蛋白，并具有原子分辨率已知的结构。用户可以一次提交一个序列，并且可以选择在三种不同的解码方法之间进行选择。该服务器报告了给定蛋白的预测拓扑，一个分数表明该蛋白是外膜β-桶蛋白的概率，跨膜链预测的后验概率以及跨膜链假定位置的图形表示与跨膜链相对于跨膜链的位置。脂质双层。
The beta-barrel outer membrane proteins constitute one of the two known structural classes of membrane proteins. Whereas there are several different web-based predictors for alpha-helical membrane proteins, currently there is no freely available prediction method for beta-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of beta-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. The server reports the predicted topology of a given protein, a score indicating the probability of the protein being an outer membrane beta-barrel protein, posterior probabilities for the transmembrane strand prediction and a graphical representation of the assumed position of the transmembrane strands with respect to the lipid bilayer.