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

拟议的研究涉及重要生物分子（如蛋白质，核酸及其复合物）的3D结构的质量。这些结构的知识在许多科学领域都是必不可少的，有助于我们了解生命和疾病过程的分子基础，设计更好的药物，提高食品，造纸或农业行业中使用的酶的效率等。来自世界各地的学术和工业研究人员将结构信息存放在PDB中，其他科学家使用这些信息来促进我们对人类健康，药物发现，农业等的了解和理解每个月，从管理PDB的四个组织的网站上下载超过2500万个PDB结构文件，wwPDB联盟。在PDB中的73000多个条目中，约86%是使用称为X射线晶体学的技术确定的，而13%来自核磁共振（NMR）spectroscopy.NMR的结构确定通常涉及数周的数据收集和复杂光谱的手动分析。与任何实验技术一样，NMR结构可能包含错误。为了确保存放在PDB中的数据是可靠的，需要进行全面的验证，告诉结构的生产者和用户他们的结构有多好（或坏），无论是在绝对值上还是与其他结构相比。这有助于核磁共振波谱分析师生成更好的模型，并使学术界或工业界的用户能够更好地判断他们想要使用的数据的质量或选择最佳数据。为了解决这个问题，wwPDB成立了专家验证工作组（VTF），该工作组将建议应使用哪些验证方法以及哪些领域仍需要进一步研究。我们的目标是改进NMR衍生结构的验证。本提案的目标是：1.在集成软件管道中实施NMR VTF的建议。这条管道将用于评估PDB中已经存在的所有NMR结构以及未来将沉积的所有结构的质量。严格评估当前NMR验证工具的实用性、范围和局限性。这将揭示为什么目前的验证方法有时会失败，除其他事项外。3.开发新的算法，程序和工具，用于验证NMR结构。在上一步中确定的任何限制和弱点将在此处解决。4.传播与验证有关的信息和新开发的验证方法，供更广泛的科学界使用。这确保了NMR光谱学家能够产生更好的模型，非专业用户也能够评估他们可用的NMR结构的质量。Kleywegt教授是欧洲蛋白质数据库（PDBe）的负责人。PDBe是wwPDB的创始成员，也是欧洲生物信息学研究所的一部分，该研究所是生物信息学研究和服务的世界领导者。PDBe在所有主要结构测定技术方面拥有广泛的专业知识，并已在实施wwPDB X射线VTF的建议。共同申请人Vuister教授是莱斯特大学（UoL）生物化学系的一部分，该系拥有3个NMR和2个X射线组。他是NMR衍生结构验证方面的领先专家，也是NMR VTF的成员。

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.