SAD phasing by OASIS-2004: case studies of dual-space fragment extension.
SAD phasing by OASIS-2004: case studies of dual-space fragment extension.
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DOI：
10.1107/s0907444906006445
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发表时间：
2006-08
期刊：
影响因子：
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通讯作者：
De-qiang Yao;Sheng Huang;Jia-Wei Wang;Yuan-xin Gu;C. Zheng;H. Fan;N. Watanabe;I. Tanaka
中科院分区：
文献类型：
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作者：
De-qiang Yao;Sheng Huang;Jia-Wei Wang;Yuan-xin Gu;C. Zheng;H. Fan;N. Watanabe;I. Tanaka
在蛋白质SAD数据处理中，采用了双空间相移原理。迭代双空间片段扩展涉及四个程序，以提高自动建模的效率。OASIS-2004被用来打破SAD实验中固有的相位模糊。在初始周期中，SAD相位二重态的识别是通过结合已知反常散射子结构的直接方法来实现的。在随后的周期中，通过结合已知的异常散射子结构和从前一周期的模型建立中获得的部分蛋白质结构的直接方法来进行识别。DM用于通过密度修正来改进直接法相。RESOLE用于初始建模，ARP/WARP用于完成结构。用三组困难的SAD数据进行的案例研究表明，该程序有利于高通量蛋白质结构的确定，并且所涉及的四个程序都对该过程做出了独特的贡献。
The principle of dual-space phasing is used in dealing with protein SAD data. Four programs are involved in iterative dual-space fragment extension to improve automatic model building. OASIS-2004 is used to break the phase ambiguity intrinsic in the SAD experiment. In the initial cycle, discrimination of SAD phase doublets is performed by the direct method incorporating the known anomalous-scattering substructure. In subsequent cycles, discrimination is performed by the direct method incorporating both the known anomalous-scattering substructure and the partial protein structure obtained from model building in the preceding cycle. DM is used to improve direct-method phases via density modification. RESOLVE is used for initial model building and ARP/wARP is used to complete the structure. Case studies with three sets of difficult SAD data showed that the procedure is beneficial to high-throughput protein-structure determination and all of the four programs involved make their unique contribution to the process.