Molecular replacement: the probabilistic approach of the program REMO09 and its applications
Molecular replacement: the probabilistic approach of the program REMO09 and its applications
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DOI：
10.1107/s0108767309035612
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发表时间：
2009-11-01
影响因子：
1.8
通讯作者：
Siliqi, Dritan
中科院分区：
文献类型：
--
作者：
Caliandro, Rocco;Carrozzini, Benedetta;Siliqi, Dritan
联合概率分布函数方法已应用于分子置换技术。旋转搜索通过相对于模型结构的计算变换旋转蛋白质的倒易晶格来执行;平移搜索通过快速傅立叶变换来执行。先验信息的几种情况下进行了研究，无论是旋转和平移步骤：e。G.对于从头算和当给定其它单体的旋转和/或平移值时，都找到单体的旋转或平移的条件概率密度。新方法已在REMO 09计划中实施，REMO 09计划是IL MILIONE全球定相包的一部分[Burla，Caliandro，Camalli，Cascarano，De Caro，Giacovazzo，Polidori，Siliqi & Spagna（2007）。J. Appl.Cryst.40，609-613]。一个大的测试结构已被用于检查新算法的效率，这被证明是显着的鲁棒性，在找到正确的解决方案，并在区分它们的噪音。一个重要的设计概念是高度自动化：REMO 09通常能够提供目标结构的可靠模型，而无需任何用户干预。
The method of joint probability distribution functions has been applied to molecular replacement techniques. The rotational search is performed by rotating the reciprocal lattice of the protein with respect to the calculated transform of the model structure; the translation search is performed by fast Fourier transform. Several cases of prior information are studied, both for the rotation and for the translation step: e. g. the conditional probability density for the rotation or the translation of a monomer is found both for ab initio and when the rotation and/or the translation values of other monomers are given. The new approach has been implemented in the program REMO09, which is part of the package for global phasing IL MILIONE [Burla, Caliandro, Camalli, Cascarano, De Caro, Giacovazzo, Polidori, Siliqi & Spagna (2007). J. Appl. Cryst. 40, 609-613]. A large set of test structures has been used for checking the efficiency of the new algorithms, which proved to be significantly robust in finding the correct solutions and in discriminating them from noise. An important design concept is the high degree of automatism: REMO09 is often capable of providing a reliable model of the target structure without any user intervention.