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

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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.