PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
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DOI：
10.1093/nar/gkl262
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发表时间：
2006-07-01
影响因子：
14.9
通讯作者：
Rost B
中科院分区：
文献类型：
--
作者：
Bigelow H;Rost B
PROFtmb预测革兰氏阴性细菌中的跨膜β桶(TMB)蛋白。对于每个查询蛋白质，PROFtmb既提供了表明蛋白质实际上包含膜桶的Z值，也提供了向上和向下的链、周质发夹和细胞外环的四态每残基标记。虽然大多数用户提交了已知含有TMBS的单个蛋白质，但一些小组提交了整个蛋白质组来筛选潜在的TMBS。对于500个残基的蛋白质，响应时间约为4分钟。PROFTMB是一种基于配置文件的隐马尔可夫模型(HMM)，其体系结构反映了TMBS的结构。在8倍交叉验证测试集上，每个残基的准确率为86%，而在60%的覆盖率下，全蛋白识别准确率为70%。PROFtmb网络服务器包括来自78个革兰氏阴性细菌基因组的所有源代码、训练数据和全蛋白质组预测，可以免费获得，无需注册。
PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. For each query protein, PROFtmb provides both a Z-value indicating that the protein actually contains a membrane barrel, and a four-state per-residue labeling of upward- and downward-facing strands, periplasmic hairpins and extracellular loops. While most users submit individual proteins known to contain TMBs, some groups submit entire proteomes to screen for potential TMBs. Response time is about 4 min for a 500-residue protein. PROFtmb is a profile-based Hidden Markov Model (HMM) with an architecture mirroring the structure of TMBs. The per-residue accuracy on the 8-fold cross-validated testing set is 86% while whole-protein discrimination accuracy was 70 at 60% coverage. The PROFtmb web server includes all source code, training data and whole-proteome predictions from 78 Gram-negative bacterial genomes and is available freely and without registration at .
影响因子：
14.9
作者：
Bigelow, HR;Petrey, DS;Rost, B
通讯作者：
Rost, B
DOI：
10.1038/86214
发表时间：
2001-04-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
--
作者：
Arora, A;Abildgaard, F;Tamm, LK
通讯作者：
Tamm, LK
影响因子：
3
作者：
Bagos PG;Liakopoulos TD;Spyropoulos IC;Hamodrakas SJ
通讯作者：
Hamodrakas SJ