Expediting topology data gathering for the TOPDB database.
Expediting topology data gathering for the TOPDB database.
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DOI：
10.1093/nar/gku1119
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发表时间：
2015-01
影响因子：
14.9
通讯作者：
Tusnády GE
中科院分区：
文献类型：
--
作者：
Dobson L;Langó T;Reményi I;Tusnády GE
跨膜蛋白拓扑数据库（Topology Data Bank of Transmembrane Proteins，TOPDB，http://topdb.enzim.ttk.mta.hu）包含实验确定的跨膜蛋白拓扑数据。最近，我们已经更新了TOPDB从几个来源，并利用一个新开发的拓扑预测算法，以确定最可靠的拓扑使用的实验结果作为约束。除了收集实验确定的拓扑数据发表在过去几年中，我们收集的拓扑结构定义的TMDET算法使用3D结构的PDBTM。将各种生物体的全局拓扑分析结果以及通过高通量技术生成的拓扑数据（如N-或O-糖基化的顺序位置）并入TOPDB数据库。此外，一个新的算法来整合分散的拓扑数据从各种公开可用的数据库和一个新的方法来衡量预测的拓扑结构的可靠性。我们表明，可靠性值高度相关的每蛋白质拓扑结构的准确性所利用的预测方法。自TOPDB数据库最后一次公开发布以来，总共收集了超过52000个新的拓扑数据和超过2600个新的跨膜蛋白。
The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM. Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database. Moreover, a new algorithm was developed to integrate scattered topology data from various publicly available databases and a new method was introduced to measure the reliability of predicted topologies. We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method. Altogether, more than 52 000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database.
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影响因子：
5.8
作者：
Hennerdal, Aron;Elofsson, Arne
通讯作者：
Elofsson, Arne
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Lomize AL;Pogozheva ID;Lomize MA;Mosberg HI
通讯作者：
Mosberg HI
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作者：
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通讯作者：
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作者：
Kozma, Daniel;Simon, Istvan;Tusnady, Gabor E.
通讯作者：
Tusnady, Gabor E.