Validation of Structures in the Protein Data Bank

Structure - Tập 25 - Trang 1916-1927 - 2017
Swanand Gore1, Eduardo Sanz García1, Pieter M.S. Hendrickx1, Aleksandras Gutmanas1, John D. Westbrook2, Huanwang Yang2, Zukang Feng2, Kumaran Baskaran3, John M. Berrisford1, Brian P. Hudson2, Yasuyo Ikegawa4, Naohiro Kobayashi4, Catherine L. Lawson2, Steve Mading3, Lora Mak1, Abhik Mukhopadhyay1, Thomas J. Oldfield1, Ardan Patwardhan1, Ezra Peisach2, Gaurav Sahni1
1Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
2RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
3BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
4PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan

Tài liệu tham khảo

Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., 66, 213, 10.1107/S0907444909052925 Adams, 2016, Outcome of the first wwPDB/CCDC/D3R ligand validation workshop, Structure, 24, 502, 10.1016/j.str.2016.02.017 Berjanskii, 2005, A simple method to predict protein flexibility using secondary chemical shifts, J. Am. Chem. Soc., 127, 14970, 10.1021/ja054842f Berman, 2000, The Protein Data Bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235 Berman, 2003, Announcing the worldwide Protein Data Bank, Nat. Struct. Biol., 10, 980, 10.1038/nsb1203-980 Brünger, 1992, Free R-value— a novel statistical quantity for assessing the accuracy of crystal structures, Nature, 355, 472, 10.1038/355472a0 Bruno, 2004, Retrieval of crystallographically-derived molecular geometry information, J. Chem. Inf. Comput. Sci., 44, 2133, 10.1021/ci049780b Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr. D Biol. Crystallogr., 66, 12, 10.1107/S0907444909042073 Dutta, 2009, Data deposition and annotation at the worldwide Protein Data Bank, Mol. Biotechnol., 42, 1, 10.1007/s12033-008-9127-7 Editorial, 2016, Where are the data?, Nat. Struct. Mol. Biol., 23, 871, 10.1038/nsmb.3307 Emsley, 2010, Features and development of coot, Acta Crystallogr. D Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493 Engh, 2001, Structure quality and target parameters, 382 Gore, 2012, Implementing an X-ray validation pipeline for the Protein Data Bank, Acta Crystallogr. D Biol. Crystallogr., 68, 478, 10.1107/S0907444911050359 Grabowski, 2016, A public database of macromolecular diffraction experiments, Acta Crystallogr. D Struct. Biol., 72, 1181, 10.1107/S2059798316014716 Groom, 2016, The cambridge structural database, Acta Crystallogr. B Struct. Sci. Cryst. Eng. Mater., 72, 171, 10.1107/S2052520616003954 Gutmanas, 2015, NMR Exchange Format: a unified and open standard for representation of NMR restraint data, Nat. Struct. Mol. Biol., 22, 433, 10.1038/nsmb.3041 Henderson, 2012, Outcome of the first electron microscopy validation task force meeting, Structure, 20, 205, 10.1016/j.str.2011.12.014 Iudin, 2016, EMPIAR: a public archive for raw electron microscopy image data, Nat. Methods, 13, 387, 10.1038/nmeth.3806 Jones, 1991, Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr. A, 47, 110, 10.1107/S0108767390010224 Joosten, 2014, The PDB_REDO server for macromolecular structure model optimization, IUCr J., 1, 213, 10.1107/S2052252514009324 Kinjo, 2017, Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures, Nucleic Acids Res., 45, D282, 10.1093/nar/gkw962 Kirchner, 2011, Objective identification of residue ranges for the superposition of protein structures, BMC Bioinformatics, 12, 1, 10.1186/1471-2105-12-170 Kleywegt, 1995, Where freedom is given, liberties are taken, Structure, 3, 535, 10.1016/S0969-2126(01)00187-3 Kleywegt, 2002, Homo crystallographicus—quo vadis?, Structure, 10, 465, 10.1016/S0969-2126(02)00743-8 Kleywegt, 2004, The Uppsala electron-density server, Acta Crystallogr. D Biol. Crystallogr., 60, 2240, 10.1107/S0907444904013253 Lagerstedt, 2013, Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB, J. Struct. Biol., 184, 173, 10.1016/j.jsb.2013.09.021 Lawson, 2016, EMDataBank unified data resource for 3DEM, Nucleic Acids Res., 44, D396, 10.1093/nar/gkv1126 Meyer, 2016, Data publication with the structural biology data grid supports live analysis, Nat. Commun., 7, 10882, 10.1038/ncomms10882 Maia, 2012, The coherent X-ray imaging data bank, Nat. Methods, 9, 854, 10.1038/nmeth.2110 Montelione, 2013, Recommendations of the wwPDB NMR validation task force, Structure, 21, 1563, 10.1016/j.str.2013.07.021 Murshudov, 1997, Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr. D Biol. Crystallogr., 53, 240, 10.1107/S0907444996012255 Padilla, 2003, A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning, Acta Crystallogr. D Biol. Crystallogr., D59, 1124, 10.1107/S0907444903007947 Parkinson, 1996, New parameters for the refinement of nucleic acid-containing structures, Acta Crystallogr. D Biol. Crystallogr., 52, 57, 10.1107/S0907444995011115 Ramachandran, 1963, Stereochemistry of polypeptide chain configurations, J. Mol. Biol., 7, 95, 10.1016/S0022-2836(63)80023-6 Read, 2011, A new generation of crystallographic validation tools for the protein data bank, Structure, 19, 1395, 10.1016/j.str.2011.08.006 Shao, 2006, Crystallographic analysis of calcium-dependent heparin binding to annexin A2, J. Biol. Chem., 281, 31689, 10.1016/S0021-9258(19)84082-6 Shao, 2017, Multivariate analyses of quality metrics for crystal structures in the protein data bank archive, Structure, 25, 458, 10.1016/j.str.2017.01.013 Ulrich, 2008, BioMagResBank, Nucleic Acids Res., 36, D402, 10.1093/nar/gkm957 Velankar, 2016, PDBe: improved accessibility of macromolecular structure data from PDB and EMDB, Nucleic Acids Res., 44, D385, 10.1093/nar/gkv1047 Wang, 2010, A probabilistic approach for validating protein NMR chemical shift assignments, J. Biomol. NMR, 47, 85, 10.1007/s10858-010-9407-y Westbrook, 2015, The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank, Bioinformatics, 31, 1274, 10.1093/bioinformatics/btu789 Wilson, 1948, Determination of absolute from relative X-Ray intensity data, Nature, 150, 152, 10.1038/150152a0 Winn, 2011, Overview of the CCP4 suite and current developments, Acta Crystallogr. D Biol. Crystallogr., 67, 235, 10.1107/S0907444910045749 Yang, 2016, DCC: a Swiss army knife for structure factor analysis and validation, J. Appl. Cryst., 49, 1081, 10.1107/S1600576716004428 Young, 2017, OneDep: unified wwPDB system for deposition, biocuration, and validation of macromolecular structures in the PDB Archive, Structure, 25, 536, 10.1016/j.str.2017.01.004