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

这项建议涉及保存结构生物学领域的研究成果和实验数据，该领域旨在确定重要生物分子的三维(3D)结构，如蛋白质和核酸。对这些结构的了解可以帮助发现新药、疾病诊断学的发展、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过程。结构数据由来自除南极洲以外的所有大洲的学术、政府和工业实验室的研究人员存储到一个单一的全球档案(蛋白质数据库或PDB)中。然后对这些数据进行注释，并公开和免费提供。在1971年开始只有7个蛋白质结构之后，PDB经历了几乎指数级的增长，并在2014年5月超过了10万个结构的里程碑。自2003年以来，PDB一直由世界蛋白质数据库(WWPDB)联盟管理，合作伙伴包括英国、美国和日本。X射线结晶学和核磁共振是结构生物学的两种主要实验方法，它们贡献了PDB中99%的结构。结构生物界的广泛共识是，生物分子的存档结构应该伴随着支持它们的实验数据。这不仅使其他科学家能够复制、验证或重新解释最初的发现，还刺激和促进了结构确定和验证的新方法的发展。自2008年以来，所有由X射线和核磁共振方法确定的结构都必须存储实验数据。然而，其他技术通常与X射线或核磁共振相结合，如今越来越多地被用于研究大型、复杂和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数据可以存储在单独的档案中(称为EMDB)。另一种日益流行的技术是小角X射线(或中子)散射(SAXS/SANS)。它可以提供有关所研究分子的整体大小和形状的信息。此外，SANS实验还可以提供各种分子相互作用形成大分子络合物时的相对位置信息。然而，WWPDB目前没有收集基础实验SAXS/SANS数据的机制。因此，世界粮食计划署的合作伙伴召集了一个小角散射技术专家工作队，就小角散射系统/SANS数据的存档问题征求意见。特别工作组强烈建议，如果这种数据与另一种技术结合使用或用于支持另一种技术，则由WWPDB收集和传播。这项建议旨在通过增加WWPDB档案软件，然后将收集的SAXS/SANS数据传播给科学界来实施这一建议。这个项目将提高我们对重要生物分子和络合物结构的描述和理解。欧洲蛋白质数据库(PDBe)是WWPDB的创始成员之一。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)在英国的分支机构。PDBe在X射线结晶学、核磁共振、低温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伙伴密切合作，并与SAXS/SANS技术方面的世界领先专家协商，执行拟议的项目。

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.