Supporting archival and dissemination of small-angle scattering data for atomistic structures in the PDB

支持PDB中原子结构的小角度散射数据的归档和传播

基本信息

  • 批准号:
    BB/M020347/1
  • 负责人:
  • 金额:
    $ 18.86万
  • 依托单位:
  • 依托单位国家:
    英国
  • 项目类别:
    Research Grant
  • 财政年份:
    2015
  • 资助国家:
    英国
  • 起止时间:
    2015 至 无数据
  • 项目状态:
    已结题

项目摘要

This proposal is concerned with preserving research results and experimental data in the field of structural biology, which aims to determine three-dimensional (3D) structures of important biological molecules, such as proteins and nucleic acids. Knowledge of these structures can aid areas such as discovery of new drugs, development of diagnostics of diseases, understanding the biology of health, disease and ageing, and optimisation of industrial processes through engineering of better enzymes. Structural data is deposited into a single global archive (the Protein Data Bank or PDB) by researchers from academic, government and industrial laboratories from all continents except Antarctica. This data is then annotated and made publicly and freely available. After starting with only 7 protein structures in 1971, the PDB experienced an almost exponential growth and in May 2014 passed the 100,000-structure milestone. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB) consortium, with partners in the UK, USA and Japan.X-ray crystallography and Nuclear Magnetic Resonance (NMR) are the main two experimental methods in structural biology, and they have contributed 99% of the structures in the PDB. There is wide consensus in the structural biology community that the archived structures of biological molecules should be accompanied by the experimental data that supports them. Not only does this enable other scientists to reproduce, verify or reinterpret the original findings, it also stimulates and facilitates the development of new methods for structure determination and validation. Since 2008, deposition of experimental data is mandatory for all structures determined by X-ray and NMR methods.However, other techniques, usually in combination with X-ray or NMR, are increasingly used nowadays to investigate the structure of large, complex and thus challenging biological systems. A popular technique is electron microscopy (EM), and experimental EM data can be deposited in a separate archive (called EMDB). Another, increasingly popular technique is small-angle X-ray (or neutron) scattering (SAXS/SANS). It can provide information on the overall size and shape of the studied molecules. SANS experiments in addition can provide information on the relative positions of various molecules when they interact to form large complexes. However, the wwPDB does not currently have a mechanism to collect the underlying experimental SAXS/SANS data. The wwPDB partners have therefore convened a task force of experts in small-angle scattering techniques (SAS TF) to get advice on archiving of SAXS/SANS data. The SAS TF strongly recommended that this data be collected and disseminated by wwPDB if it was used in conjunction with or in support of another technique.This proposal aims to implement this recommendation by developing additions to the wwPDB archival software, and then disseminating the collected SAXS/SANS data to the scientific community. This project will improve our description and understanding of structures of important biological molecules and complexes.The Protein Data Bank in Europe (PDBe) is a founding member of wwPDB. PDBe is part of the European Bioinformatics Institute (EMBL-EBI), the UK-based outstation of the European Molecular Biology Laboratory (EMBL). PDBe has strong expertise in X-ray crystallography, NMR, cryo-electron microscopy and software development. PDBe will pursue the proposed project in close collaboration with its international wwPDB partners and in consultation with world-leading experts in the SAXS/SANS techniques.
该提案涉及保存结构生物学领域的研究成果和实验数据,旨在确定重要生物分子(例如蛋白质和核酸)的三维(3D)结构。了解这些结构可以帮助发现新药、开发疾病诊断、了解健康、疾病和衰老的生物学,以及通过设计更好的酶来优化工业流程等领域。来自除南极洲以外各大洲的学术、政府和工业实验室的研究人员将结构数据存入一个全球档案库(蛋白质数据库或 PDB)。然后对这些数据进行注释并公开免费提供。自 1971 年开始只有 7 个蛋白质结构后,PDB 经历了近乎指数级的增长,并于 2014 年 5 月突破了 100,000 个结构的里程碑。自2003年以来,PDB由世界蛋白质数据库(wwPDB)联盟管理,合作伙伴来自英国、美国和日本。X射线晶体学和核磁共振(NMR)是结构生物学中主要的两种实验方法,它们贡献了PDB中99%的结构。结构生物学界达成广泛共识,生物分子的存档结构应附有支持它们的实验数据。这不仅使其他科学家能够重现、验证或重新解释原始发现,还刺激和促进了结构测定和验证新方法的开发。自 2008 年以来,对于所有通过 X 射线和 NMR 方法测定的结构,都必须提供实验数据。然而,其他技术(通常与 X 射线或 NMR 相结合)现在越来越多地用于研究大型、复杂且具有挑战性的生物系统的结构。一种流行的技术是电子显微镜 (EM),实验 EM 数据可以存放在单独的档案中(称为 EMDB)。另一种日益流行的技术是小角度 X 射线(或中子)散射 (SAXS/SANS)。它可以提供有关所研究分子的总体尺寸和形状的信息。此外,SANS 实验还可以提供各种分子相互作用形成大型复合物时的相对位置信息。然而,wwPDB 目前没有收集底层实验 SAXS/SANS 数据的机制。因此,wwPDB 合作伙伴召集了一个由小角度散射技术 (SAS TF) 专家组成的工作组,以获取有关 SAXS/SANS 数据归档的建议。 SAS TF 强烈建议,如果这些数据与其他技术结合使用或支持其他技术,则由 wwPDB 收集和传播。该提案旨在通过开发 wwPDB 档案软件的附加功能来实施此建议,然后将收集到的 SAXS/SANS 数据传播给科学界。该项目将改善我们对重要生物分子和复合物结构的描述和理解。欧洲蛋白质数据库 (PDBe) 是 wwPDB 的创始成员。 PDBe 是欧洲生物信息学研究所 (EMBL-EBI) 的一部分,该研究所是欧洲分子生物学实验室 (EMBL) 位于英国的分站。 PDBe 在 X 射线晶体学、核磁共振、冷冻电子显微镜和软件开发方面拥有丰富的专业知识。 PDBe 将与其国际 wwPDB 合作伙伴密切合作,并与 SAXS/SANS 技术领域的世界领先专家协商,推进拟议项目。

项目成果

期刊论文数量(10)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
The archiving and dissemination of biological structure data.
  • DOI:
    10.1016/j.sbi.2016.06.018
  • 发表时间:
    2016-10
  • 期刊:
  • 影响因子:
    6.8
  • 作者:
    Berman, Helen M.;Burley, Stephen K.;Kleywegt, Gerard J.;Markley, John L.;Nakamura, Haruki;Velankar, Sameer
  • 通讯作者:
    Velankar, Sameer
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
  • DOI:
    10.1016/j.str.2017.01.004
  • 发表时间:
    2017-03-07
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Young JY;Westbrook JD;Feng Z;Sala R;Peisach E;Oldfield TJ;Sen S;Gutmanas A;Armstrong DR;Berrisford JM;Chen L;Chen M;Di Costanzo L;Dimitropoulos D;Gao G;Ghosh S;Gore S;Guranovic V;Hendrickx PMS;Hudson BP;Igarashi R;Ikegawa Y;Kobayashi N;Lawson CL;Liang Y;Mading S;Mak L;Mir MS;Mukhopadhyay A;Patwardhan A;Persikova I;Rinaldi L;Sanz-Garcia E;Sekharan MR;Shao C;Swaminathan GJ;Tan L;Ulrich EL;van Ginkel G;Yamashita R;Yang H;Zhuravleva MA;Quesada M;Kleywegt GJ;Berman HM;Markley JL;Nakamura H;Velankar S;Burley SK
  • 通讯作者:
    Burley SK
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
  • DOI:
    10.1093/database/bay002
  • 发表时间:
    2018-01-01
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Young JY;Westbrook JD;Feng Z;Peisach E;Persikova I;Sala R;Sen S;Berrisford JM;Swaminathan GJ;Oldfield TJ;Gutmanas A;Igarashi R;Armstrong DR;Baskaran K;Chen L;Chen M;Clark AR;Di Costanzo L;Dimitropoulos D;Gao G;Ghosh S;Gore S;Guranovic V;Hendrickx PMS;Hudson BP;Ikegawa Y;Kengaku Y;Lawson CL;Liang Y;Mak L;Mukhopadhyay A;Narayanan B;Nishiyama K;Patwardhan A;Sahni G;Sanz-García E;Sato J;Sekharan MR;Shao C;Smart OS;Tan L;van Ginkel G;Yang H;Zhuravleva MA;Markley JL;Nakamura H;Kurisu G;Kleywegt GJ;Velankar S;Berman HM;Burley SK
  • 通讯作者:
    Burley SK
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
  • DOI:
    10.1093/nar/gkx1070
  • 发表时间:
    2018-01-04
  • 期刊:
  • 影响因子:
    14.9
  • 作者:
    Mir S;Alhroub Y;Anyango S;Armstrong DR;Berrisford JM;Clark AR;Conroy MJ;Dana JM;Deshpande M;Gupta D;Gutmanas A;Haslam P;Mak L;Mukhopadhyay A;Nadzirin N;Paysan-Lafosse T;Sehnal D;Sen S;Smart OS;Varadi M;Kleywegt GJ;Velankar S
  • 通讯作者:
    Velankar S
Resolution of ab initio shapes determined from small-angle scattering.
  • DOI:
    10.1107/s2052252516016018
  • 发表时间:
    2016-11-01
  • 期刊:
  • 影响因子:
    3.9
  • 作者:
    Tuukkanen AT;Kleywegt GJ;Svergun DI
  • 通讯作者:
    Svergun DI
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Gerard Kleywegt其他文献

Gerard Kleywegt的其他文献

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{{ truncateString('Gerard Kleywegt', 18)}}的其他基金

Public archiving and data integration in the era of multi-modal imaging
多模态成像时代的公共归档和数据集成
  • 批准号:
    MR/P019544/1
  • 财政年份:
    2017
  • 资助金额:
    $ 18.86万
  • 项目类别:
    Research Grant
Integrating 3D biological data on scales from molecules to cells
整合从分子到细胞尺度的 3D 生物数据
  • 批准号:
    MR/L007835/1
  • 财政年份:
    2014
  • 资助金额:
    $ 18.86万
  • 项目类别:
    Research Grant
CRESTANO - Common REst api for Structural ANnotation
CRESTANO - 用于结构注释的通用 REst api
  • 批准号:
    BB/K016970/1
  • 财政年份:
    2013
  • 资助金额:
    $ 18.86万
  • 项目类别:
    Research Grant
GENOME-3D: a UK network providing structure-based annotations for genotype to phenotype studies
GENOME-3D:英国网络,为基因型到表型研究提供基于结构的注释
  • 批准号:
    BB/I02576X/1
  • 财政年份:
    2012
  • 资助金额:
    $ 18.86万
  • 项目类别:
    Research Grant
Validation of biomacromolecular structures determined by NMR spectroscopy and deposited in the Protein Data Bank
通过核磁共振波谱法验证生物大分子结构并存入蛋白质数据库
  • 批准号:
    BB/J007471/1
  • 财政年份:
    2012
  • 资助金额:
    $ 18.86万
  • 项目类别:
    Research Grant
The Electron Microscopy Data Bank
电子显微镜数据库
  • 批准号:
    BB/G022577/1
  • 财政年份:
    2009
  • 资助金额:
    $ 18.86万
  • 项目类别:
    Research Grant
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
  • 财政年份:
    2007
  • 资助金额:
    $ 18.86万
  • 项目类别:
    Research Grant

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  • 批准号:
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Imaging Core
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神经影像信息学工具和资源协作:外展、基础设施和维护
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  • 财政年份:
    2019
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Neuroimaging Informatics Tools and Resources Collaboratory: Outreach, Infrastructure and Maintenance
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The Lung PCA: A Multi-Dimensional Atlas of Pulmonary Premalignancy
肺 PCA:肺癌前病变的多维图谱
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