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Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule (see example in the image), come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties. Proteins and nucleic acids are the workhorses of biology, providing the necessary chemical reactions, structural organization, growth, mobility, reproduction, and environmental sensitivity. Essential to their biological functions are the detailed 3D structures of the molecules and the changes in those structures. To understand and control those functions, we need accurate knowledge about the models that represent those structures, including their many strong points and their occasional weaknesses. End-users of macromolecular models include clinicians, teachers and students, as well as the structural biologists themselves, journal editors and referees, experimentalists studying the macromolecules by other techniques, and theoreticians and bioinformaticians studying more general properties of biological molecules. Their interests and requirements vary, but all benefit greatly from a global and local understanding of the reliability of the models. ==Historical summary== Macromolecular crystallography was preceded by the older field of small-molecule x-ray crystallography (for structures with less than a few hundred atoms). Small-molecule diffraction data extends to much higher resolution than feasible for macromolecules, and has a very clean mathematical relationship between the data and the atomic model. The residual, or R-factor, measures the agreement between the experimental data and the values back-calculated from the atomic model. For a well-determined small-molecule structure the R-factor is nearly as small as the uncertainty in the experimental data (well under 5%). Therefore that one test by itself provides most of the validation needed, but a number of additional consistency and methodology checks are done by automated software as a requirement for small-molecule crystal structure papers submitted to the International Union of Crystallography (IUCr) journals such as Acta Crystallographica section B or C. Atomic coordinates of these small-molecule structures are archived and accessed through the Cambridge Structural Database (CSD) or the Crystallography Open Database (COD). The first macromolecular validation software was developed around 1990, for proteins. It included Rfree cross-validation for model-to-data match, bond length and angle parameters for covalent geometry, and sidechain and backbone conformational criteria. For macromolecular structures, the atomic models are deposited in the Protein Data Bank (PDB), still the single archive of this data. The PDB was established in the 1970s at Brookhaven National Laboratory, moved in 2000 to the () (Research Collaboration for Structural Biology) centered at Rutgers, and expanded in 2003 to become the (wwPDB ) (worldwide Protein Data Bank), with access sites added in Europe (()) and Asia (()), and with NMR data handled at the (BioMagResBank (BMRB) ) in Wisconsin. Validation rapidly became standard in the field, with further developments described below. *Obviously needs expansion * A large boost was given to the applicability of comprehensive validation for both x-ray and NMR as of February 1, 2008, when the worldwide Protein Data Bank (wwPDB) made mandatory the deposition of experimental data along with atomic coordinates. Since 2012 strong forms of validation have been in the process of being adopted for (wwPDB deposition ) from recommendations of the wwPDB Validation Task Force committees for x-ray crystallography, for NMR, for SAXS (small-angle x-ray scattering), and for cryoEM (cryo-Electron Microscopy). 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Structure validation」の詳細全文を読む スポンサード リンク
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