Unified data resource for NMR spectral and PDB data via and enhanced deposition visualisation and validation autodep system development

该提案的目标是确保欧洲的核磁共振研究人员能够以类似于美国RCSB和BMRB开发的方式访问方便的本地核磁共振结构沉积系统和所有相关数据。我们将建立在我们完善的数据库系统上，我们计划利用我们的基础设施，在此基础上建立核磁共振光谱数据沉积和检索。我们已经开发了基于web的Java/XML沉积系统，用于PDB的AutoDep4和用于EMDB的EmDep，在此基础上，我们将扩展这些系统，以允许将3D结构数据存档和路由到PDB的坐标信息和BMRB的NMR光谱数据。此外，作为wwPDB的成员，默沙东集团致力于处理更大比例的PDB提交，作为全球伙伴关系的一部分。核磁共振数据包含有关生物大分子结构和动力学的丰富信息。然而，以一种有意义的方式提取这些信息往往是困难的。例如，某些蛋白质主链原子的化学位移值可以直接用于确定蛋白质的二级结构，但由于化学位移值是在分子采用的所有不同构象之间的平均，因此更灵活的主链区域或侧链原子的化学位移很难解释。此外，在溶液核磁共振中很少使用核磁共振信号宽度等信息。目前的沉积系统对核磁共振光谱数据的存款人和潜在用户都提出了一些主要的困难。对于大多数存款人来说，为了存档一组实验，坐标和光谱数据是彼此半独立的。特别是，输入实验相关元数据的耗时过程必须进行两次，通过两个不同的进程，每个进程收集相关实验数据的不同子集。对于坐标数据的潜在用户，链接到核磁共振光谱数据，没有简单的显示选项，以查看这些数据在网络上。我们还将扩展我们的分子结构可视化和分析软件AstexViewer@MSD-EBI的功能，用于显示和分析与3D结构和化学性质相关的NMR数据，以提供快速，基于对象的复杂分析访问。通过增强这些现有的工具，调整到特定的NMR应用程序，我们将为NMR结构社区提供强大的应用程序。MSD数据库包含与生物大分子的结构坐标直接相关的核磁共振信息，为能够以更有意义的方式将核磁共振数据与结构联系起来开辟了令人兴奋的前景。特别是从结构的角度来看，限制是至关重要的，可视化与结构相关的限制分布将是本提案的重要成果。我们将对从BMRB数据库中提取的光谱数据进行“大规模”结构相关分析，并将其与与蛋白质化学位移数据相关的化学实体的特定MSD数据相结合。随着与分子动力学直接相关的弛豫数据越来越多，进行包含尽可能多数据的大规模分析变得至关重要。这项拨款将产生两个主要成果。首先，我们将开发一个统一的沉积界面，用于沉积与PDB特定数据和BMRB特定数据的NMR大分子结构测定相关的所有数据。其次，我们将开发一个访问门户，用于可视化和分析这些数据，适合核磁共振社区应用于广泛的问题。

The goal of this proposal is to ensure that NMR investigators in Europe have access to a convenient local system of deposition of NMR structures and all associated data in a manner similar to that developed by the RCSB and BMRB in the United States. We will build on our well-established database systems, and we plan to use our infrastructure by building on top of this for NMR Spectral data deposition and retrieval. We have developed web based Java/XML deposition systems, AutoDep4 for the PDB and the EmDep for EMDB and from this base we will extend these systems to allow for the archival and routing of 3D structure data to both the PDB for coordinate information and to the BMRB for NMR spectral data. In addition as a member of the wwPDB the MSD group is committed to process a greater proportion of PDB submissions as part of the global partnership. NMR data contains a wealth of information about the structure and dynamics of biological macromolecules. It is, however, often difficult to extract this information in a meaningful way. For example, the chemical shift values of certain protein backbone atoms can be directly used to determine the secondary structure of a protein, but because chemical shift values are averaged between all the different conformations a molecule adopts the chemical shifts of more flexible backbone regions or side chain atoms are much harder to interpret. In addition, information about, for example, the width of NMR signals is seldom used in solution NMR. The current deposition system presents a number of major difficulties for both depositors and potential users of NMR spectral data. For most depositors, coordinates and spectral data are deposited semi-independently of one another in order to archive a set of experiments. In particular, the time-consuming process of entering metadata related to the experiment must be performed twice, through two different processes, each of which collects a different subset of the relevant experimental data. For potential users of coordinate data the linkage to NMR spectral data there is no simple display option to view such data over the web. We will also extend the functionality of our visualisation and analysis software for molecular structures, AstexViewer@MSD-EBI, for the display and analysis of NMR data in relation to 3D structure and chemical properties to give a fast, object-based access to complex analyses. By enhancing these existing tools, tuned to specific NMR applications, we will provide powerful applications for the NMR structural community. The MSD database contains NMR information that is directly linked to the structure coordinates of biological macromolecules and opens exciting prospects for being able to relate NMR data to the structures in a more meaningful way. In particular from a structure point of view, the restraints are crucial and to visualise the distribution of restraints in relation to structure will be an important deliverable in this proposal. We will carry out a 'large scale' structure related analysis of the spectral data extracted from the BMRB database combining this with specific MSD data on chemical entities in relation to protein chemical shift data. As more relaxation data, which is directly related to the dynamics of the molecule, becomes available it is crucial that large-scale analyses are performed that incorporates as much data as possible. There will be two major results from this grant. First we will have developed a unified deposition interface for the deposition of all data related to macromolecular structure determination by NMR for both PDB specific data and BMRB specific data. Second we will have developed an access portal for the visualisation and analysis of this data suitable for the NMR community to apply to a wide range of problems.