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

通过增强的沉积可视化和验证 autodep 系统开发，统一 NMR 光谱和 PDB 数据的数据资源

• 批准号: BB/E007511/1
• 负责人: Gerard Kleywegt
• 金额: $ 58.83万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FE007511%2F1
• 关键词: Unified; data; resource; NMR; spectral

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.

该提案的目标是确保欧洲的 NMR 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 NMR 结构沉积系统和所有相关数据。我们将建立在完善的数据库系统的基础上，并计划在此基础上使用我们的基础设施进行核磁共振波谱数据存储和检索。我们开发了基于 Web 的 Java/XML 沉积系统、用于 PDB 的 AutoDep4 和用于 EMDB 的 EmDep，并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（用于坐标信息）和 BMRB（用于 NMR 光谱数据）。此外，作为 wwPDB 的成员，MSD 集团致力于处理更大比例的 PDB 提交，作为全球合作伙伴关系的一部分。核磁共振数据包含有关生物大分子的结构和动力学的丰富信息。然而，以有意义的方式提取这些信息通常很困难。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所有不同构象之间的平均值，因此分子采用更灵活的主链区域或侧链原子的化学位移更难以解释。此外，溶液 NMR 中很少使用有关 NMR 信号宽度等信息。当前的沉积系统给 NMR 光谱数据的沉积者和潜在用户带来了许多主要困难。对于大多数存储者来说，坐标和光谱数据彼此半独立地存储，以便存档一组实验。特别是，输入与实验相关的元数据的耗时过程必须通过两个不同的过程执行两次，每个过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来说，与 NMR 光谱数据的链接没有简单的显示选项来通过网络查看此类数据。我们还将扩展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，从而提供基于对象的快速复杂分析。通过增强这些现有工具，并针对特定的 NMR 应用进行调整，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 NMR 信息，并为能够以更有意义的方式将 NMR 数据与结构关联起来开辟了令人兴奋的前景。特别是从结构的角度来看，约束至关重要，并且可视化与结构相关的约束分布将是该提案的重要成果。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。随着更多与分子动力学直接相关的弛豫数据变得可用，进行大规模分析以包含尽可能多的数据至关重要。这笔赠款将产生两个主要成果。首先，我们将开发一个统一的沉积接口，用于沉积与 NMR 大分子结构测定相关的所有数据，包括 PDB 特定数据和 BMRB 特定数据。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 NMR 社区应用到广泛的问题。

项目成果

Straightforward and complete deposition of NMR data to the PDBe.

• DOI: 10.1007/s10858-010-9439-3
• 发表时间: 2010-10
• 期刊: Journal of biomolecular NMR
• 影响因子: 2.7
• 作者: Penkett CJ;van Ginkel G;Velankar S;Swaminathan J;Ulrich EL;Mading S;Stevens TJ;Fogh RH;Gutmanas A;Kleywegt GJ;Henrick K;Vranken WF
• 通讯作者: Vranken WF

Recommendations of the wwPDB NMR Validation Task Force.

• DOI: 10.1016/j.str.2013.07.021
• 发表时间: 2013-09-03
• 期刊: STRUCTURE
• 影响因子: 5.7
• 作者: Montelione, Gaetano T.;Nilges, Michael;Bax, Ad;Guentert, Peter;Herrmann, Torsten;Richardson, Jane S.;Schwieters, Charles D.;Vranken, Wim F.;Vuister, Geerten W.;Wishart, David S.;Berman, Helen M.;Kleywegt, Gerard J.;Markley, John L.
• 通讯作者: Markley, John L.

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.

• DOI: 10.1002/prot.24213
• 发表时间: 2013-04
• 期刊: Proteins
• 影响因子: 2.9
• 作者: Hendrickx PM;Gutmanas A;Kleywegt GJ
• 通讯作者: Kleywegt GJ

The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.

• DOI: 10.1007/s10858-009-9378-z
• 发表时间: 2009-12
• 期刊: Journal of biomolecular NMR
• 影响因子: 2.7
• 作者: Doreleijers JF;Vranken WF;Schulte C;Lin J;Wedell JR;Penkett CJ;Vuister GW;Vriend G;Markley JL;Ulrich EL
• 通讯作者: Ulrich EL

PDBe: Protein Data Bank in Europe.

• DOI: 10.1093/nar/gkt1180
• 发表时间: 2014-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Gutmanas A;Alhroub Y;Battle GM;Berrisford JM;Bochet E;Conroy MJ;Dana JM;Fernandez Montecelo MA;van Ginkel G;Gore SP;Haslam P;Hatherley R;Hendrickx PM;Hirshberg M;Lagerstedt I;Mir S;Mukhopadhyay A;Oldfield TJ;Patwardhan A;Rinaldi L;Sahni G;Sanz-García E;Sen S;Slowley RA;Velankar S;Wainwright ME;Kleywegt GJ
• 通讯作者: Kleywegt GJ