PDB_REDO: automated re-refinement of X-ray structure models in the PDB.
PDB_REDO: automated re-refinement of X-ray structure models in the PDB.
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DOI：
10.1107/s0021889809008784
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发表时间：
2009-06-01
影响因子：
6.1
通讯作者：
Vriend G
中科院分区：
文献类型：
--
作者：
Joosten RP;Salzemann J;Bloch V;Stockinger H;Berglund AC;Blanchet C;Bongcam-Rudloff E;Combet C;Da Costa AL;Deleage G;Diarena M;Fabbretti R;Fettahi G;Flegel V;Gisel A;Kasam V;Kervinen T;Korpelainen E;Mattila K;Pagni M;Reichstadt M;Breton V;Tickle IJ;Vriend G
大多数以前沉积的X射线结构可以通过应用当前的精细化方法来改进。结构生物学、同源建模和合理的药物设计都需要精确的三维大分子坐标。然而，蛋白质数据库(PDB)中的坐标并不都是使用最新的实验和计算方法获得的。在这项研究中，提出了一种对PDB中现有结构模型进行自动求精的方法。一个有16个 807PDB条目的大规模基准表明，它们可以在与沉积的实验X射线数据的拟合方面以及在几何质量方面进行改进。再求精协议使用TLS模型来描述原子的协同运动。生成的结构模型可通过pdb_redo数据库(http://www.cmbi.ru.nl/pdb_redo/).)获得网格计算技术被用来克服这一努力的计算要求。
The majority of previously deposited X-ray structures can be improved by applying current refinement methods. Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.