Archiving and disseminating integrative structure models
Archiving and disseminating integrative structure models
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DOI：
10.1007/s10858-019-00264-2
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发表时间：
2019-07-01
影响因子：
2.7
通讯作者：
Berman，Helen M.
中科院分区：
文献类型：
--
作者：
Vallat，Brinda;Webb，Benjamin;Berman，Helen M.
单个结构表征方法的适用性、准确性和精确度的局限性有时可以通过依赖于所有可用来源的信息（包括所有可用的实验数据和先前模型）的综合建模方法来克服。开源集成建模平台（IMP）是一个软件，它实现了集成建模的所有计算方面。为了最大限度地发挥综合结构的影响，应该公开这些坐标，就像基于X射线晶体学、核磁共振光谱学和电子显微镜的结构一样。此外，相关的实验数据和建模协议也应该存档，以便可以很容易地复制原始结果。最后，重要的是，整合结构作为其出版和沉积的一部分得到验证。一些研究小组已经开发了软件来实现综合建模，并产生了一些结构，促使形成一个综合/混合方法工作队。根据该工作组的建议，用于原子PDB结构的现有PDBx/mmCIF数据表示已被扩展，以满足归档综合结构模型的要求。该IHM字典添加了灵活的模型表示，包括粗粒度化、多状态和/或按时间或其他顺序相关的模型以及多个输入实验信息源。一个名为PDB-Dev的原型存档系统（ https://pdb-dev.wwpdb.org ）也被创建用于存档综合结构模型，以及Python库，以便于处理PDBx/mmCIF格式的综合模型。
Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format.