Validation of biomacromolecular structures determined by NMR spectroscopy and deposited in the Protein Data Bank

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The proposed research addresses the quality of 3D structures of important biological molecules such as proteins, nucleic acids and their complexes. Knowledge of these structures is essential in many areas of science and helps us understand the molecular basis of life and disease processes, design better drugs, improve the efficiency of enzymes used in the food, paper or agriculture industry, etc. Structural data is archived in a single, freely accessible, global archive called the Protein Data Bank (PDB). The structural information is deposited in the PDB by academic and industrial researchers from all over the world and is used by other scientists to advance our knowledge and understanding of human health, drug discovery, agriculture, etc. Every month, more than 25 million PDB structure files are downloaded from the websites of the four organisations that manage the PDB, the wwPDB consortium. Of more than 73000 entries in the PDB, about 86% were determined using a technique called X-ray crystallography, while 13% come from Nuclear Magnetic Resonance (NMR) spectroscopy.Structure determination by NMR typically involves weeks of data collection and manual analysis of complex spectra. As with any experimental technique, NMR structures may contain errors. To ensure that the data deposited in the PDB are reliable, there is a need for comprehensive validation, which tells both producers and users of structures how good (or bad) their structures are, both in absolute terms and compared to other structures. This helps NMR spectroscopists to produce better models, and structure users in academia or industry to better judge the quality of the data they want to use or to select the best data for their purposes. To address this issue, expert validation task forces (VTFs) have been set up by the wwPDB, which will recommend what validation methods should be used and which areas still require further research.Our aim is to improve validation of NMR-derived structures. The objectives of this proposal are:1. To implement the recommendations of the NMR VTF in an integrated software pipeline. This pipeline will be used to assess the quality of all NMR structures already in the PDB and of all structures that will be deposited in the future.2. To critically assess the utility, scope and limitations of current NMR validation tools. This will reveal why current validation methods sometimes fail, amongst other things.3. To develop new algorithms, procedures and tools for validation of NMR structures. Any limitations and weaknesses identified in the previous step will be addressed here.4. To disseminate validation-related information and newly developed validation methods for use by the wider scientific community. This ensures that NMR spectroscopists will be able to produce better models, and that non-expert users will be able to assess the quality of NMR structures available to them.One applicant, Prof. Kleywegt is head of the Protein Data Bank in Europe (PDBe). PDBe is a founding member of the wwPDB and is part of the European Bioinformatics Institute, a world leader in bioinformatics research and services. PDBe has extensive expertise in all major structure determination techniques and is already implementing the recommendations of the wwPDB X-ray VTF. The co-applicant , Prof. Vuister, is part of the Department of Biochemistry of the University of Leicester (UoL), home to 3 NMR- and 2 X-ray groups. He is a leading expert on validation of NMR-derived structures and is a member of the NMR VTF.