PDBTM: Protein Data Bank of transmembrane proteins after 8 years.
PDBTM: Protein Data Bank of transmembrane proteins after 8 years.
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DOI：
10.1093/nar/gks1169
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发表时间：
2013-01
影响因子：
14.9
通讯作者：
Tusnády GE
中科院分区：
文献类型：
--
作者：
Kozma D;Simon I;Tusnády GE
PDBTM数据库（可在http://pdbtm.enzim.hu获得）是蛋白质数据库的第一个全面和最新的跨膜蛋白选择，于2004年推出。该数据库由TMDET算法创建并不断更新，该算法能够仅使用其3D原子坐标区分跨膜和非跨膜蛋白。TMDET算法还可以定位跨膜蛋白在脂质双层中的空间位置。在过去的8年中，不仅PDBTM数据库的规模从2000个条目稳步增长到1700个条目，而且除了众所周知的α-螺旋束和β-桶结构之外，还发现了新的结构元素。自第一次发布以来，已经解决了许多“外来”跨膜蛋白质结构，这使得有必要定义这些新的结构元素，例如数据库中的膜环或界面螺旋。本文报告了PDBTM数据库自首次发布以来添加的新功能，以及我们目前为保持数据库更新和易于使用所做的努力，以便它可以继续作为科学界的基本资源。
The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ∼400 to 1700 entries but also new structural elements have been identified, in addition to the well-known α-helical bundle and β-barrel structures. Numerous ‘exotic’ transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community.
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影响因子：
3.5
作者：
Iwamoto, T;Nakamura, TY;Shigekawa, M
通讯作者：
Shigekawa, M
影响因子：
14.9
作者：
Kozma, Daniel;Simon, Istvan;Tusnady, Gabor E.
通讯作者：
Tusnady, Gabor E.
影响因子：
14.9
作者：
Gromiha MM;Yabuki Y;Suresh MX;Thangakani AM;Suwa M;Fukui K
通讯作者：
Fukui K
影响因子：
13.8
作者：
Henrick, K;Thornton, JM
通讯作者：
Thornton, JM
影响因子：
64.8
作者：
Jordan, P;Fromme, P;Krauss, N
通讯作者：
Krauss, N