The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.
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DOI：
10.1007/s10858-009-9378-z
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发表时间：
2009-12
影响因子：
2.7
通讯作者：
Ulrich EL
中科院分区：
文献类型：
--
作者：
Doreleijers JF;Vranken WF;Schulte C;Lin J;Wedell JR;Penkett CJ;Vuister GW;Vriend G;Markley JL;Ulrich EL
几个试验性实验已经表明，通过应用现代软件和新方案，可以预期旧NMR结构的改进（Nabuurs等人，Proteins 55：483-186; Nederveen等人，Proteins 59：662-672; Saccenti和Rosato，J Biomol NMR 40：251-261）。最近的大规模X射线研究还表明，现代软件可以显著提高几年前沉积的X射线结构的质量（Joosten等人，J. Appl Crystallogr 42：376-384; Sanderson，Nature 459：1038-1039）。三维坐标的重新计算要求原始实验数据是可用的和完整的，并且在语义和语法上是正确的，或者至少是正确的，足以被重建。由于多种原因，包括缺乏标准、实验数据的异质性和许多NMR实验类型，解析与蛋白质NMR结构相关的大部分原始存放的NMR实验数据文件是不切实际的。这使得这些结构的三维坐标的自动重新计算以及由此的改进变得不切实际。在这里，我们描述了一个大规模的国际合作努力，使所有存放的实验NMR数据语义和语法均匀，从而有利于进一步的研究。在这一过程中，5 266个条目中共有4 014个被“清理”。1,387个条目需要人工干预。在自动解析旧的和新存放的文件方面的持续努力正在稳步减少这一比例。已清理的数据文件可从http://restraintsgrid.bmrb.wisc.edu上的NMR约束网格获得。本文的在线版本（doi：10.1007/s10858-009-9378-z）包含补充材料，可供授权用户使用。
Several pilot experiments have indicated that improvements in older NMR structures can be expected by applying modern software and new protocols (Nabuurs et al. in Proteins 55:483–186,; Nederveen et al. in Proteins 59:662–672,; Saccenti and Rosato in J Biomol NMR 40:251–261,). A recent large scale X-ray study also has shown that modern software can significantly improve the quality of X-ray structures that were deposited more than a few years ago (Joosten et al. in J. Appl Crystallogr 42:376–384,; Sanderson in Nature 459:1038–1039,). Recalculation of three-dimensional coordinates requires that the original experimental data are available and complete, and are semantically and syntactically correct, or are at least correct enough to be reconstructed. For multiple reasons, including a lack of standards, the heterogeneity of the experimental data and the many NMR experiment types, it has not been practical to parse a large proportion of the originally deposited NMR experimental data files related to protein NMR structures. This has made impractical the automatic recalculation, and thus improvement, of the three dimensional coordinates of these structures. We here describe a large-scale international collaborative effort to make all deposited experimental NMR data semantically and syntactically homogeneous, and thus useful for further research. A total of 4,014 out of 5,266 entries were ‘cleaned’ in this process. For 1,387 entries, human intervention was needed. Continuous efforts in automating the parsing of both old, and newly deposited files is steadily decreasing this fraction. The cleaned data files are available from the NMR restraints grid at http://restraintsgrid.bmrb.wisc.edu. The online version of this article (doi:10.1007/s10858-009-9378-z) contains supplementary material, which is available to authorized users.
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影响因子：
3.5
作者：
NILGES, M;CLORE, GM;GRONENBORN, AM
通讯作者：
GRONENBORN, AM
影响因子：
2.9
作者：
Vranken, WF;Boucher, W;Laue, ED
通讯作者：
Laue, ED
影响因子：
5.6
作者：
CLORE, GM;BRUNGER, AT;GRONENBORN, AM
通讯作者：
GRONENBORN, AM
影响因子：
14.9
作者：
Henrick K;Feng Z;Bluhm WF;Dimitropoulos D;Doreleijers JF;Dutta S;Flippen-Anderson JL;Ionides J;Kamada C;Krissinel E;Lawson CL;Markley JL;Nakamura H;Newman R;Shimizu Y;Swaminathan J;Velankar S;Ory J;Ulrich EL;Vranken W;Westbrook J;Yamashita R;Yang H;Young J;Yousufuddin M;Berman HM
通讯作者：
Berman HM
影响因子：
14.9
作者：
Ulrich EL;Akutsu H;Doreleijers JF;Harano Y;Ioannidis YE;Lin J;Livny M;Mading S;Maziuk D;Miller Z;Nakatani E;Schulte CF;Tolmie DE;Kent Wenger R;Yao H;Markley JL
通讯作者：
Markley JL