Research Collaboratory for Structural Bioinformatics, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA 94143, USA.
Structure. 2018 Jun 5;26(6):894-904.e2. doi: 10.1016/j.str.2018.03.011. Epub 2018 Apr 12.
Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain "hybrid" or "integrative" structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms. Here we present the development of data standards and a prototype system for archiving I/H models. The data standards provide the definitions required for representing I/H models that span multiple spatiotemporal scales and conformational states, as well as spatial restraints derived from different experimental techniques. Based on these data definitions, we have built a prototype system called PDB-Dev, which provides the infrastructure necessary to archive I/H structural models. PDB-Dev is now accepting structures and is open to the community for new submissions.
生物学中的基本过程是由大型的高分子组装体完成的，其结构通常难以通过传统方法来确定。越来越多的研究人员将测量数据与来自几种互补方法的计算信息相结合，以获得大分子及其组装体的“混合”或“综合”结构模型。由于缺乏标准的数据表示和处理机制，这些集成/混合（I/H）模型并未被 PDB 存档。在这里，我们介绍了数据标准的开发和用于存档 I/H 模型的原型系统。这些数据标准为表示跨越多个时空尺度和构象状态的 I/H 模型以及来自不同实验技术的空间限制提供了所需的定义。基于这些数据定义，我们构建了一个名为 PDB-Dev 的原型系统，该系统提供了存档 I/H 结构模型所需的基础设施。PDB-Dev 现在接受结构，并向社区开放新的提交。
