Liu Zhi-Jie, Lin Dawei, Tempel Wolfram, Praissman Jeremy L, Rose John P, Wang Bi-Cheng
Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia, USA.
Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):520-7. doi: 10.1107/S0907444905003239. Epub 2005 Apr 20.
The determination of protein structures on a genomic scale requires both computing capacity and efficiency increases at many stages along the complex process. By combining bioinformatics workflow-management techniques, cluster-based computing and popular crystallographic structure-determination software packages, an efficient and powerful new tool for structural biology/genomics has been developed. Using the workflow manager and a simple web interface, the researcher can, in a few easy steps, set up hundreds of structure-determination jobs, each using a slightly different set of program input parameters, thus efficiently screening parameter space for the optimal input-parameter combination, i.e. a set of parameters that leads to a successful structure determination. Upon completion, results from the programs are harvested, analyzed, sorted based on success and presented to the user via the web interface. This approach has been applied with success in more than 30 cases. Examples of successful structure determinations based on single-wavelength scattering (SAS) are described and include cases where the 'rational' crystallographer-based selection of input parameters values had failed.
在基因组规模上确定蛋白质结构，在这个复杂过程的许多阶段都需要计算能力和效率的提升。通过结合生物信息学工作流程管理技术、基于集群的计算以及流行的晶体学结构测定软件包，已经开发出了一种高效且强大的结构生物学/基因组学新工具。利用工作流程管理器和简单的网络界面，研究人员可以通过几个简单步骤设置数百个结构测定任务，每个任务使用略有不同的一组程序输入参数，从而有效地筛选参数空间以寻找最佳输入参数组合，即一组能成功确定结构的参数。完成后，程序的结果会被收集、分析、根据成功情况进行排序，并通过网络界面呈现给用户。这种方法已在30多个案例中成功应用。文中描述了基于单波长散射（SAS）成功确定结构的例子，包括基于晶体学家“合理”选择输入参数值却失败的情况。
