The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.
The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.
复制标题
DOI：
10.1007/s10858-015-9953-4
复制
发表时间：
2015-08
影响因子：
2.7
通讯作者：
Vuister GW
中科院分区：
文献类型：
--
作者：
Rosato A;Vranken W;Fogh RH;Ragan TJ;Tejero R;Pederson K;Lee HW;Prestegard JH;Yee A;Wu B;Lemak A;Houliston S;Arrowsmith CH;Kennedy M;Acton TB;Xiao R;Liu G;Montelione GT;Vuister GW
第二轮社区范围内的倡议“通过NMR进行蛋白质自动结构测定的关键评估”（CASD-NMR-2013）包括10个盲目标数据集，包括未处理的光谱数据、指定的化学位移列表和未指定的NOESY峰和RDC列表，这些数据集以管理（即手动优化）或非管理（即自动生成）的形式提供。十个结构计算程序，仅使用全自动协议，为十个目标生成了总共164个三维结构（条目），有时使用策划和未策划的列表为单个目标生成多个条目。可通过将这些条目与每一目标的相应人工解算结构进行比较来确定条目的准确性，而在提供数据时，人工解算结构尚不可用。在整个数据集中，提交的所有条目中有71%相对于参考NMR结构的准确度优于1.5 μ m。基于NOESY峰列表的方法获得了更好的结果，对于某些程序，高达100%的条目在1.5 μ m阈值内。然而，一些方法对于使用未经管理的NOESY峰列表的一些靶标不收敛。超过90%的条目的准确度优于上一轮CASD-NMR-2010中使用的更宽松的阈值2.5 μ m。未策划与策划峰值生成的条目之间的比较显示，在两种计算收敛的情况下，后者只有边际改进。本文的在线版本（doi：10.1007/s10858-015-9953-4）包含补充材料，可供授权用户使用。
The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged. The online version of this article (doi:10.1007/s10858-015-9953-4) contains supplementary material, which is available to authorized users.