Gerard Kleywegt

Gerard Kleywegt

Senior Team Leader: Protein Data Bank in Europe and Kleywegt Research Group

PhD University of Utrecht, 1991. Postdoctoral Fellow, then assistant professor, research scientist and associate professor, University of Uppsala, 1992-2009. Coordinator, then Programme Director of the Swedish Structural Biology Network, 1996-2009. Professor of Structural Molecular Biology, University of Uppsala, 2009.

Tel:+ 44 (0) 1223 492 663 / Fax:+ 44 (0) 1223 494 468

Research

Find out about research activity in the Kleywegt research group

Kleywegt team

The Protein Data Bank in Europe (PDBe), led by Prof. Gerard Kleywegt, is the European partner in the Worldwide Protein Data Bank organisation (wwPDB), which maintains the single international archive for biomacromolecular structure data. The other wwPDB partners are the Research Collaboratory for Structural Bioinformatics (RCSB) and Biological Magnetic Resonance Bank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj). PDBe is a deposition and annotation site for the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB). The major goal of PDBe is to provide integrated structural data resources that evolve with the needs of biologists. To that end, the PDBe team endeavours to: handle deposition and annotation of structural data expertly; provide an integrated resource of high-quality macromolecular structures and related data; and maintain in-house expertise in all the major structure-determination techniques.

Publications

2013

Cryo-electron microscopy: a primer for the non-microscopist
Milne, J. L., Borgnia M. J., Bartesaghi A., Tran E. E., Earl L. A., Schauder D. M., Lengyel J., Pierson J., PATWARDHAN A., and Subramaniam S.
FEBS Journal. Volume 280, Number 1, (2013), p.28-45 doi: 10.1111/febs.12078
Genome 3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Lewis, T. E., Sillitoe I., Andreeva A., Blundell T. L., Buchan D. W. A., Chothia C., Cuff A., DANA J. M., Filippis I., Gough J., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D499-D507 doi: 10.1093/nar/gks1266
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
VELANKAR, S., DANA J. M., JACOBSEN J., GINKEL VAN G., Gane P. J., LUO J., Oldfield T. J., O'Donovan C., Martin M. J., and KLEYWEGT G. J.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D483-D489 doi: 10.1093/nar/gks1258
UniChem: a unified chemical structure cross-referencing and identifier tracking system
CHAMBERS, J., DAVIES M., GAULTON A., HERSEY A., VELANKAR S., Petryszak R., HASTINGS J., Bellis L., MCGLINCHEY S., and OVERINGTON J. P.
Journal of Cheminformatics. Volume 5, (2013), p.3 doi: 10.1186/1758-2946-5-3
Crystal structure of the entire respiratory complex I
Baradaran, R., Berrisford J. M., Minhas G. S., and Sazanov L. A.
Nature. Volume 494, Number Issue 7438, (2013), p.443-448 doi: 10.1038/nature11871
The role of structural bioinformatics resources in the era of integrative structural biology
GUTMANAS, A., Oldfield T. J., PATWARDHAN A., SEN S., VELANKAR S., and KLEYWEGT G. J.
Acta Crystallographica Section D. Number D69, (2013), p.710-721 doi: 10.1107/S0907444913001157
BioJS: an open source JavaScript framework for biological data visualization
Gómez, J., García L. J., Salazar G. A., Villaveces J., GORE S., Garcia A., Martin M. J., Launay G., ALCANTARA R., del-Toro N., et al.
Bioinformatics. Volume 29, Issue 8, (2013), p.1103-1104 doi: 10.1093/bioinformatics/btt100
The EBI enzyme portal
ALCANTARA, R., ONWUBIKO J., CAO H., MATOS DE P., Cham J. A., JACOBSEN J., HOLLIDAY G. L., FISCHER J. D., RAHMAN S. A., Jassal B., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D773-D780 doi: 10.1093/nar/gks1112
Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB
Trewhella, J., Henrickson W. A., KLEYWEGT G. J., Sali A., Sato M., Schwede T., Svergun D. I., Tainer J. A., Westbrook J., and Berman H. M.
Structure. Volume 21, Number Issue 6, (2013), p.875-881 doi: 10.1016/j.str.2013.04.020
Vivaldi: visualisation and validation of biomacromolecular NMR structures from the PDB
Hendrickx, P. M. S., GUTMANAS A., and KLEYWEGT G. J.
Proteins. Volume 81, (2013), p.583-591 doi: 10.1002/prot.24213
The Future of the Protein Data Bank
Berman, H. M., KLEYWEGT G. J., Nakamura H., and Markley J. L.
Biopolymers. Volume 99, Issue Number 3, (2013), p.218-222 doi: 10.1002/bip.22132

2012

Towards Generating a Corpus Annotated for Prokaryote-Drug Relations
Ying, Y., Kafkas S., Conroy M., and REBHOLZ-SCHUHMANN D.
Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine. (2012), doi: 10.5167/uzh-64476
Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data
Rosato, A., Aramini J. M., Arrowsmith C., Bagaria A., Baker D., Cavalli A., Doreleijers J. F., Eletsky A., Giachetti A., Guerry P., et al.
Structure. Volume 20, Number Issue 2, (2012), p.227-236. doi: 10.1016/j.str.2012.01.002
WeNMR: Structural Biology on the Grid
Wassenaar, T. A., van Dijk M., Loureiro-Ferreira N., van der Schot G., de Vries S. J., Schmitz C., van der Zwan J., Boelens R., Giachetti A., Ferella L., et al.
Journal of Grid Computing. Volume 10, (2012), p.743-767 doi: 10.1007/s10723-012-9246-z
ACPYPE - AnteChamber PYthon Parser interfacE
SILVA, SOUSA DA A. W., and VRANKEN W. F.
BMC Research Notes. Volume 5, (2012), p.367-374 doi: 10.1186/1756-0500-5-367
Protein Structure Validation Using Side-Chain Chemical Shifts
Sahakyan, A. B., Cavalli A., VRANKEN W. F., and Vendruscolo M.
The Journal of Physical Chemistry B. Volume 116, Number 16, (2012), p.4754-4759 doi: 10.1021/jp2122054
Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts
Camilloni, C., Simone De A., VRANKEN W. F., and Vendruscolo M.
Biochemistry. Volume 51, Number 11, (2012), p.2224-2231 doi: 10.1021/bi3001825
The Worldwide Protein Data Bank
Berman, H. M., Henrick K., KLEYWEGT G. J., Nakamura H., and Markley J. L.
International Tables for Crystallography. Volume F, Number ch. 24.1, (2012), p.827-832 doi: 10.1107/97809553602060000896
CING: an integrated residue-based structure validation program suite
Doreleijers, J. F., SILVA SOUSA DA A. W., Krieger E., Nabuurs S. B., Spronk C. A., Stevens T. J., VRANKEN W. F., Vriend G., and Vuister G. W.
Journal of Biomolecular NMR. Volume 54, Number 3, (2012), p.267-283 doi: 10.1007/s10858-012-9669-7
Validation of protein crystal structures
KLEYWEGT, G. J.
International Tables for Crystallography. Volume F, Issue ch.21.1, Number ch.21.1, (2012), p.649-661 doi: 10.1107/97809553602060000879
Structure of the signal transduction protein TRAP (target of RNAIII-activating protein)
Henrick, K., and Hirshberg M.
Acta Crystallographica Section F. Volume 68, Number Part 7, (2012), p.744-750 doi: 10.1107/S1744309112020167
Potential 2-aminosuccinimide structures in mollusc proteins
GARAVELLI, J., and Hirshberg M.
Protein Science. Volume 21, (2012), p.130 doi: 10.1002/pro.2113
The 2010 Cryo-EM Modeling Challenge
Ludtke, S. J., Lawson C. L., KLEYWEGT G. J., Berman H., and Chiu W.
Biopolymers. Volume 97, Number 9, (2012), p.651-654 doi: 10.1002/bip.22081
Data management challenges in three-dimensional EM
PATWARDHAN, A., Carazo J. M., Carragher B., Henderson R., Heymann J. B., Hill E., Jensen G. J., LAGERSTEDT I., Lawson C. L., Ludtke S. J., et al.
Nature Structural & Molecular Biology. Volume 19, Number 12, (2012), p.1203-1207 doi: 10.1038/nsmb.2426
Implementing an X-ray validation pipeline for the Protein Data Bank
GORE, S., VELANKAR S., and KLEYWEGT G. J.
Acta Crystallographica Section D. Volume 68, Number Pt 4, (2012), p.478-483 doi: 10.1107/S0907444911050359
OMERO: flexible, model-driven data management for experimental biology
Allan, C., Burel J. M., Moore J., Blackburn C., Linkert M., Loynton S., Macdonald D., Moore W. J., Neves C., Patterson A., et al.
Nature Methods. Volume 9, Number 3, (2012), p.245-253 doi: 10.1038/nmeth.1896
Outcome of the First Electron Microscopy Validation Task Force Meeting
Henderson, R., Sali A., Baker M. L., Carragher B., Devkota B., Downing K. H., Egelman E. H., Feng Z., Frank J., Grigorieff N., et al.
Structure . Volume 20, Number 2, (2012), p.205-214 doi: 10.1016/j.str.2011.12.014
PDBe: Protein Data Bank in Europe
VELANKAR, S., ALHROUB Y., BEST C., CABOCHE S., CONROY M. J., DANA J. M., MONTECELO FERNANDEZ M. A., GINKEL VAN G., Golovin A., GORE S. P., et al.
Nucleic Acids Research. Volume 40 , Issue Database issue, Number Database issue, (2012), p.D445-D452 doi: 10.1093/nar/gkr998
The Protein Data Bank at 40: reflecting on the past to prepare for the future
Berman, H. M., KLEYWEGT G. J., Nakamura H., and Markley J. L.
Structure . Volume 20, Number 3, (2012), p.391-396 doi: 10.1016/j.str.2012.01.010
On the need for an international effort to capture, share and use crystallization screening data
Newman, J., Bolton E. E., Muller-Dieckmann J., Fazio V. J., Gallagher D. T., Lovell D., Luft J. R., Peat T. S., Ratcliffe D., Sayle R. A., et al.
Acta Crystallographica Section F. Volume 68, Number Pt 3, (2012), p.253-258 doi: 10.1107/S1744309112002618

2011

A new generation of crystallographic validation tools for the Protein Data Bank
Read, R. J., Adams P. D., Arendall W. B., Brunger A. T., Emsley P., Joosten R. P., KLEYWEGT G. J., Krissinel E. B., Lüttel T., Otwinowski Z., et al.
Structure. Volume 19, Number Issue 10, (2011), p.1395-1412 doi: 10.1016/j.str.2011.08.006
Structures of sequential open states in a symmetrical opening transition of the TolC exit duct
Pei, X-Y, Hinchliffe P., SYMMONS M. F., Koronakis E., Benz R., Hughes C., and Koronakis V.
Proceedings of the National Academy of Sciences. Volume 108, Issue 5, (2011), p.2112-2117 doi: 10.1073/pnas.1012588108
The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory
Morris, C., Pajon A., Griffiths S. L., Daniel E., Savitsky M., Lin B., Diprose J. M., A. da Silva Wilter, Pilicheva K., Troshin P., et al.
Acta Crystallographica Section D. Volume 67, (2011), p.249-260 doi: 10.1107/S0907444911007943
Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines - Workshop Introduction
Ludtke, S. J., Lawson C. L., KLEYWEGT G. J., Berman H. M., and Chiu W.
Pacific Symposium on Biocomputing. Volume 16, (2011), p.369-373 doi: 10.1142/9789814335058_0039
A novel strategy for NMR resonance assignment and protein structure determination
Lemak, A., GUTMANAS A., Chitayat S., Karra M., Farès C., Sunnerhagen M., and Arrowsmith C. H.
Journal of Biomolecular NMR. Volume 49, Number Issue 1, (2011), p.27-38 doi: 10.1007/s10858-010-9458-0
EMDataBank.org: unified data resource for CryoEM
Lawson, C. L., Baker M. L., BEST C., Bi C., Dougherty M., Feng P., GINKEL VAN G., Devkota B., LAGERSTEDT I., Newman R. H., et al.
Nucleic Acids Research. Volume 39, Number Database issue, (2011), p.D456-D464 doi: 10.1093/nar/gkq880
EUROCarbDB: An open-access platform for glycoinformatics
von der Lieth, C-W, A. Freire Ardá, Blank D., Campbell M. P., Fogh R. H., Damerell D. A., Dell A., Dwek R. A., Ernst B., Fogh R., et al.
Glycobiology. Volume 21, Number Issue 4, (2011), p.493-502 doi: 10.1093/glycob/cwq188
The Protein Data Bank in Europe (PDBe): bringing structure to biology
VELANKAR, S., and KLEYWEGT G. J.
Acta Crystallographica Section D. Volume 67, (2011), p.324-330 doi: 10.1107/S090744491004117X
PDBe: Protein Data Bank in Europe
VELANKAR, S., ALHROUB Y., Alili A., BEST C., Boutselakis H. C., CABOCHE S., CONROY M. J., DANA J. M., GINKEL VAN G., Golovin A., et al.
Nucleic Acids Research. Volume 39, Number Database issue, (2011), p.D402-D410 doi: 10.1093/nar/gkq985
Assymetric synthesis and conformational analysis by NMR spectroscopy and MD of Aba- and α-MeAba-containing demorphin analogues
Vandormael, B., De Wachter R., Martins J. C., Hendrickx P. M. S., Keresztes A., Ballet S., Mallareddy J. R., Tóth F., Tóth G., and Tourwé D.
ChemMedChem. Volume 6, Number Issue 11, (2011), p.2035-2047 doi: 10.1002/cmdc.201100314
Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures
Sahakyan, A. B., VRANKEN W. F., Cavalli A., and Vendruscolo M.
Angewandte Chemie International Edition. Volume 50, (2011), p.9620-9623 doi: 10.1002/anie.201101641
Structure-based prediction of methyl chemical shifts in proteins
Sahakyan, A. B., VRANKEN W. F., Cavalli A., and Vendruscolo M.
Journal of Biomolecular NMR. Volume 50, Number (Issue 4), (2011), p.331-346 doi: 10.1007/s10858-011-9524-2
Macromolecular complexes in crystals and solutions
Krissinel, E.
Acta Crystallographica Section D. Volume 67, Number Part 4, (2011), p.376-385 doi: 10.1107/S0907444911007232
Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures
Bernard, A., VRANKEN W. F., Bardiaux B., Nilges M., and Malliavin T. E.
Proteins. Volume 79, (2011), p.1525-1537 doi: 10.1002/prot.22980
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
ARANDA, B., Blankenburg H., KERRIEN S., Brinkman F. S. L., Ceol A., Chautard E., DANA J. M., Rivas De Las J., DUMOUSSEAU M., Galeota E., et al.
Nature Methods. Volume 8, Number Issue 7, (2011), p.528-529 doi: 10.1038/nmeth.1637
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
Doreleijers, J. F., VRANKEN W. F., Schulte C., Markley J. L., Ulrich E. L., Vriend G., and Vuister G. W.
Nucleic Acids Research. Volume 40, Number Database issue, (2011), p.D519-D524 doi: 10.1093/nar/gkr1134
Structural bioinformatics: current status and future directions
GORE, S. P., VELANKAR S., and KLEYWEGT G. J.
Proceedings of the 29th Leeds Annual Statistical Research Workshop. (2011), p.65-69 doi:

2010

Straightforward and complete deposition of NMR data to the PDBe
PENKETT, C. J., GINKEL VAN G., VELANKAR S., Swaminathan J., Ulrich E. L., Mading S., Stevens T. J., Fogh R. H., GUTMANAS A., KLEYWEGT G. J., et al.
Journal of Biomolecular NMR. Volume 48, Number Issue 2, (2010), p.85-92 doi: 10.1007/s10858-010-9439-3
Unified data resource for Cryo-EM
Lawson, C.L.
Methods in Enzymology . Volume 483, (2010), p.73-90 doi: 10.1016/S0076-6879(10)83004-6
Validation of archived chemical shifts through atomic coordinates
Rieping, W., and VRANKEN W. F.
Proteins. Volume 78, Number Issue 3, (2010), p.2482-2489 doi: 10.1002/prot.22756
Towards proteome–wide interaction models using the proteochemometrics approach
Strömbergsson, H., Lapins M., KLEYWEGT G. J., and Wikberg J. E.
Molecular Informatics. Volume 29, Number Issue 6-7, (2010), p.499-508 doi: 10.1002/minf.201000052
Crystal contacts as nature’s docking solutions
Krissinel, E. B.
Journal of Computational Chemistry. Volume 31, Number Issue 1, (2010), p.133-143 doi: 10.1002/jcc.21303
Diversity of monomers in non-ribosomal peptides
CABOCHE, S., Leclère V., Pupin M., Kucherov G., and Jacques P.
Journal of Bacteriology. Volume 192, Number Issue 19, (2010), p.5143-5150 doi: 10.1128/JB.00315-10
Digital archives for molecular microscopy
BEST, C.
Proceedings of the 1st International Digital Preservation Interoperability Framework Symposium. (2010), doi: 10.1145/2039263.2039267
Safeguarding the integrity of protein archive
Berman, H. M., KLEYWEGT G. J., Nakamura H., Markley J. L., and Burley S. K.
Nature. Volume 463, Number Issue 7280, (2010), p.425 doi: 10.1038/463425c
YhgC protects Bacillus anthracis from oxidative stress
Kiran, M. D., Bala S., Hirshberg M., and Balaban N.
International Journal of Artificial Organs. Volume 33, Number Issue 9, (2010), p.590-607 doi:
Practical application of bioinformatics by the multidisciplinary VIZIER consortium
Gorbalenya, A. E., Lieutaud P., Harris M. R., Coutard B., Canard B., KLEYWEGT G. J., Kravchenko A. A., Samborskiy D. V., Sidorov I. A., Lentovich A. M., et al.
Antiviral Research. Volume 87, Number Issue 2, (2010), p.95-110 doi: 10.1016/j.antiviral.2010.02.005
MEMOPS: data modelling and automatic code generation
Fogh, R. H., Boucher W., Ionides J. M., VRANKEN W. F., Stevens T. J., and Laue E. D.
Journal of Integrative Bioinformatics. Volume 7, Number Issue 3, (2010), p.123 doi: 10.2390/biecoll-jib-2010-123
Integration of chemical information with protein sequences and 3D structures
Golovin, A., Henrick K., and Kleywegt G.
Journal of Cheminformatics. Volume 2, Issue Suppl. 1, (2010), doi: 10.1186/1758-2946-2-S1-O17

2009

Case-controlled structure validation
Read, R. J., and KLEYWEGT G. J.
Acta Crystallographica Section D. Volume 65, Number Part 2, (2009), p.140-147 doi: 10.1107/S0907444908041085
COCO: a simple tool to enrich the representation of conformational variability in NMR structures
Laughton, C. A., Orozco M., and VRANKEN W. F.
Proteins. Volume 75, Number Issue 1, (2009), p.206-216 doi: 10.1002/prot.22235
CASD-NMR: critical assessment of automated structure determination by NMR
Rosato, A., Bagaria A., Baker D., Bardiaux B., Cavalli A., Doreleijers J. F., Giachetti A., Guerry P., Güntert P., Herrmann T., et al.
Nature Methods. Volume 6, Number Issue 9, (2009), p.625-626 doi: 10.1038/nmeth0909-625
Relationship between chemical shift value and accessible surface area for all amino acid atoms
VRANKEN, W. F., and Rieping W.
BMC Structural Biology. Volume 9, (2009), p.20 doi: 10.1186/1472-6807-9-20
PDBe: Protein Data Bank in Europe
VELANKAR, S., BEST C., Beuth B., Boutselakis C. H., Cobley N., SILVA SOUSA DA A. W., Dimitropoulos D., Golovin A., Hirshberg M., John M., et al.
Nucleic Acids Research. Volume 38, Number Database issue, (2009), p.D308-D317 doi: 10.1093/nar/gkp916
A chemogenomics view on protein-ligand spaces
Strömbergsson, H., and KLEYWEGT G. J.
BMC Bioinformatics. Volume 10, Number Supplement 6, (2009), p.S13 doi: 10.1186/1471-2105-10-S6-S13
On vital aid: the why, what and how of validation
KLEYWEGT, G. J.
Acta Crystallographica Section D. Volume 65, Number Part 2, (2009), p.134-139 doi: 10.1107/S090744490900081X
Applications of Graph Theory in Chemo- and Bioinformatics
Dimitropoulos, D., Golovin A., John M., and Krissinel E.
Analysis of Complex Networks. (2009), p.chapter 9, 221-244 doi: 10.1002.1002/9/9783527981.ch9
Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins
Simone, De A., Cavalli A., Hsu S. T., VRANKEN W. F., and Vendruscolo M.
Journal of the American Chemical Society. Volume 131, Number Issue 45, (2009), p.16332-16333 doi: 10.1021/ja904937a
The Worldwide Protein Data Bank
Berman, H. M., Henrick K., Nakamura H., and Markley J. L.
Structural Bioinformatics. (2009), p.chapter 11, 293-303. doi:
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries
Doreleijers, J. F., VRANKEN W. F., Schulte C., Lin J., Wedell J. R., PENKETT C. J., Vuister G. W., Vriend G., Markley J. L., and Ulrich E. L.
Journal of Biomolecular NMR. Volume 45, Number Issue 4, (2009), p.389-396 doi: 10.1007/s10858-009-9378-z
Chemical substructure search in SQL
Golovin, A., and Henrick K.
Journal of Chemical Information and Modeling. Volume 49, Number Issue 1, (2009), p.22-27 doi: 10.1021/ci8003013
Data Deposition and Annotation at the Worldwide Protein Data Bank
Dutta, S., Burkhardt K., Young J., SWAMINATHAN G. J., Matsuura T., Henrick K., Nakamura H., and Berman H. M.
Molecular Biotechnology. Volume 42, Number Issue 1, (2009), p.1-13 doi: 10.1007/s12033-008-9127-7
Unifying biological image formats with HDF5
Dougherty, M. T., Folk M. J., Zadok E., Bernstein H. J., Bernstein F. C., Eliceiri K. W., Benger W., and BEST C.
Communications of the ACM. Volume 52, Number Issue 10, (2009), p.42-47 doi: 10.1145/1562764.1562781

Services

BioMedBridges
PDBe
PDBe EM Resources
PDBe NMR Resources
SIFTS

Team members

Younes Alhroub
Gary Battle
John Berrisford
Matthew Conroy
Jose Dana
Manuel Fernandez Montecelo
Swanand Gore
Aleksandras Gutmanas
Pauline Haslam
Pieter Hendrickx
Miriam Hirshberg
Ingvar Lagerstedt
Saqib Mir
Abhik Mukhopadhyay
Tom Oldfield
Ardan Patwardhan
Gaurav Sahni
Eduardo Sanz Garcia
Sanchayita Sen
Robert Slowley
Glen van Ginkel
Sameer Velankar
Michael Wainwright