Gerard Kleywegt

Last updated
Gerard Kleywegt
Born
Gerrit Jacob Kleijwegt

1962 (age 61–62)
Rozenburg, Nederland
NationalityDutch
Alma mater University of Utrecht
Scientific career
Fields
Institutions European Bioinformatics Institute
University of Upsala
Thesis Computer-assisted assignment of 2D and 3D NMR spectra of proteins (Computer-ondersteunde toekenning van 2D en 3D NMR spectra van eiwitten)  (1991)
Website http://www.ebi.ac.uk/about/people/gerard-kleywegt

Gerard Jacob Kleywegt (born 5 June 1962, in Rozenburg) is a Dutch X-ray crystallographer and the former team leader of the Protein Data Bank in Europe at the EBI; [1] [2] [3] [4] a member of the Worldwide Protein Data Bank. [5] [6]

Contents

Education

Kleywegt obtained his PhD from the University of Utrecht in 1991.

Career

After his PhD, Kleywegt did postdoctoral research with Alwyn Jones at Uppsala University. [7] [8] before moving to the EBI.

Research

Kleywegt's research focuses on protein crystallography [9] [10] [11] and the Protein Data Bank. [12] [13] [14] [15] [16] [17] [18]

Related Research Articles

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). These structural data are obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organisations.

<span class="mw-page-title-main">Structural Classification of Proteins database</span> Biological database of proteins

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<span class="mw-page-title-main">Thioredoxin</span> Class of reduction–oxidation proteins

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The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank, now succeeded by the mmCIF format. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which has kept data on biological macromolecules in the newer PDBx/mmCIF file format since 2014.

<span class="mw-page-title-main">Tom Blundell</span> British biochemist

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<span class="mw-page-title-main">Crystallographic Information File</span> File format for crystallographic data

Crystallographic Information File (CIF) is a standard text file format for representing crystallographic information, promulgated by the International Union of Crystallography (IUCr). CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on Crystallographic Data and the IUCr Commission on Journals. The file format was initially published by Hall, Allen, and Brown and has since been revised, most recently versions 1.1 and 2.0. Full specifications for the format are available at the IUCr website. Many computer programs for molecular viewing are compatible with this format, including Jmol.

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<span class="mw-page-title-main">Janet Thornton</span> British bioinformatician and academic

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<span class="mw-page-title-main">ProtCID</span>

The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins.

<span class="mw-page-title-main">Steven E. Brenner</span> American biologist and academic

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<span class="mw-page-title-main">WeNMR</span> Worldwide e-Infrastructure for NMR spectroscopy and structural biology

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<span class="mw-page-title-main">Structure validation</span> Process of evaluating 3-dimensional atomic models of biomacromolecules

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<span class="mw-page-title-main">Macromolecular Crystallographic Information File</span> File format used for macromolecular structure data

The Macromolecular Crystallographic Information File (mmCIF) also known as PDBx/mmCIF is a standard text file format for representing macromolecular structure data, developed by the International Union of Crystallography (IUCr) and the Protein Data Bank It is an extension of the Crystallographic Information File (CIF), specifically for macromolecular data, such as proteins and nucleic acids, incorporating elements from the PDB file format.

References

  1. ↑ "Looking back on 2016".
  2. ↑ "Gerard Kleywegt research group page at the EBI". Archived from the original on 2014-10-20.
  3. ↑ Garwoord, Jeremy (May 2009) "A Guardian of Structural Integrity". Lab Times. pp. 19-23
  4. ↑ Berman, H. M.; Kleywegt, G. J.; Nakamura, H.; Markley, J. L.; Burley, S. K. (2010). "Safeguarding the integrity of protein archive". Nature. 463 (7280): 425. doi:10.1038/463425c. PMC   4456675 . PMID   20110969.
  5. ↑ Lewis, T. E.; Sillitoe, I; Andreeva, A; Blundell, T. L.; Buchan, D. W.; Chothia, C; Cozzetto, D; Dana, J. M.; Filippis, I; Gough, J; Jones, D. T.; Kelley, L. A.; Kleywegt, G. J.; Minneci, F; Mistry, J; Murzin, A. G.; Ochoa-Montaño, B; Oates, M. E.; Punta, M; Rackham, O. J.; Stahlhacke, J; Sternberg, M. J.; Velankar, S; Orengo, C (2015). "Genome3D: Exploiting structure to help users understand their sequences". Nucleic Acids Research. 43 (Database issue): D382-6. doi:10.1093/nar/gku973. PMC   4384030 . PMID   25348407.
  6. ↑ Lewis, T. E.; Sillitoe, I; Andreeva, A; Blundell, T. L.; Buchan, D. W.; Chothia, C; Cuff, A; Dana, J. M.; Filippis, I; Gough, J; Hunter, S; Jones, D. T.; Kelley, L. A.; Kleywegt, G. J.; Minneci, F; Mitchell, A; Murzin, A. G.; Ochoa-Montaño, B; Rackham, O. J.; Smith, J; Sternberg, M. J.; Velankar, S; Yeats, C; Orengo, C (2013). "Genome3D: A UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains". Nucleic Acids Research. 41 (Database issue): D499-507. doi:10.1093/nar/gks1266. PMC   3531217 . PMID   23203986.
  7. ↑ Jones, T. A.; Kleywegt, G. J. (2007). "Experimental Data for Structure Papers". Science. 317 (5835): 194–195. doi:10.1126/science.317.5835.194c. PMID   17626864.
  8. ↑ Kleywegt, G. J.; Jones, T. A. (1996). "Phi/psi-chology: Ramachandran revisited". Structure. 4 (12): 1395–400. doi: 10.1016/s0969-2126(96)00147-5 . PMID   8994966.
  9. ↑ Read, R. J.; Adams, P. D.; Arendall Wb, 3rd; Brunger, A. T.; Emsley, P; Joosten, R. P.; Kleywegt, G. J.; Krissinel, E. B.; Lütteke, T; Otwinowski, Z; Perrakis, A; Richardson, J. S.; Sheffler, W. H.; Smith, J. L.; Tickle, I. J.; Vriend, G; Zwart, P. H. (2011). "A new generation of crystallographic validation tools for the protein data bank". Structure. 19 (10): 1395–412. doi:10.1016/j.str.2011.08.006. PMC   3195755 . PMID   22000512.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  10. ↑ Read, R. J.; Kleywegt, G. J. (2009). "Case-controlled structure validation". Acta Crystallographica Section D. 65 (Pt 2): 140–7. doi:10.1107/S0907444908041085. PMC   2631636 . PMID   19171969.
  11. ↑ Kleywegt, G. J.; Read, R. J. (1997). "Not your average density". Structure . 5 (12): 1557–69. doi: 10.1016/s0969-2126(97)00305-5 . PMID   9438862.
  12. ↑ Montelione, G. T.; Nilges, M; Bax, A; Güntert, P; Herrmann, T; Richardson, J. S.; Schwieters, C. D.; Vranken, W. F.; Vuister, G. W.; Wishart, D. S.; Berman, H. M.; Kleywegt, G. J.; Markley, J. L. (2013). "Recommendations of the wwPDB NMR Validation Task Force". Structure. 21 (9): 1563–70. doi:10.1016/j.str.2013.07.021. PMC   3884077 . PMID   24010715.
  13. ↑ Berman, H. M.; Kleywegt, G. J.; Nakamura, H; Markley, J. L. (2013). "How community has shaped the Protein Data Bank". Structure. 21 (9): 1485–91. doi:10.1016/j.str.2013.07.010. PMC   4435976 . PMID   24010707.
  14. ↑ Berman, H. M.; Kleywegt, G. J.; Nakamura, H; Markley, J. L. (2013). "The future of the protein data bank". Biopolymers. 99 (3): 218–22. doi:10.1002/bip.22132. PMC   3684242 . PMID   23023942.
  15. ↑ Berman, H. M.; Kleywegt, G. J.; Nakamura, H; Markley, J. L. (2012). "The Protein Data Bank at 40: Reflecting on the past to prepare for the future". Structure. 20 (3): 391–6. doi:10.1016/j.str.2012.01.010. PMC   3501388 . PMID   22404998.
  16. ↑ Berman, H. M.; Kleywegt, G. J.; Nakamura, H.; Markley, J. L.; Burley, S. K. (2010). "Safeguarding the integrity of protein archive". Nature. 463 (7280): 425. doi:10.1038/463425c. PMC   4456675 . PMID   20110969.
  17. ↑ Berman, H. M.; Kleywegt, G. J.; Nakamura, H; Markley, J. L. (2014). "The Protein Data Bank archive as an open data resource". Journal of Computer-Aided Molecular Design. 28 (10): 1009–14. doi:10.1007/s10822-014-9770-y. PMC   4196035 . PMID   25062767.
  18. ↑ Berman, H. M.; Burley, S. K.; Kleywegt, G. J.; Nakamura, H; Markley, J. L. (2014). "Response to on prompt update of literature references in the Protein Data Bank". Acta Crystallographica Section D. 70 (Pt 10): 2780. doi:10.1107/S1399004714020513. PMC   4984264 . PMID   25286863.
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