Sameer Velankar

Sameer Velankar

Team Leader, PDBe content and integration

PhD, Indian Institute of Science, 1997. Postdoctoral researcher, Oxford University, UK, 1997-2000. At EMBL-EBI since 2000.

Tel:+44 (0)1223 494 646 / Fax:+44 (0)1223 494 468

Velankar team

As a founding member of the Worldwide Protein Data Bank (wwPDB), the Protein Data Bank in Europe (PDBe) manages the worldwide biomacromolecular structure archive, the Protein Data Bank (PDB). The wwPDB partners accept and annotate worldwide depositions of biomacromolecular structures determined using X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, 3D Electron Microscopy (EM) and other structure-determination methods. PDBe is a founding member of EMDataBank, which manages the deposition and annotation of EM data in EMDB. PDBe aims to ensure that this important resource truly serves the needs of the biomedical community. The PDBe content and integration team, led by Dr Sameer Velankar, works to improve the web interface so that users can make the most of existing tools and services. The team designs new tools as needed in order to make structural data available and accessible to
 all. In the context of the SIFTS project, the team integrates structural data with other biological data to facilitate discovery. These integrated data form the basis for many query interfaces that allow biomacromolecular structure data to be presented in its biological context. Specific focus areas are: data integrity, data quality, integration and data dissemination to the non-expert biomedical community.

Publications

2013

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
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
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
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
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

2012

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
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
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

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
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
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
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
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

2009

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

2008

Remediation of the Protein Data Bank archive
Henrick, K., Feng Z., Bluhm W.F., Dimitropoulos D., Doreleijgers J.F., Dutta S., Flippen-Anderson J.L., Ionides J., Kamada C., Krissinel E., et al.
Nucleic Acids Research. Volume 36, Issue Database issue, (2008), p.D426-D433 doi: 10.1093/nar/gkm937

2006

E-MSD: improving data deposition and structure quality
Tagari, M., Tate J., Swaminathan G.J., Newman R., Naim A., Vranken W., Kapopoulou A., Hussain A., Fillon J., Henrick K., et al.
Nucleic Acids Research. Volume 34, Issue Database issue, (2006), p.D287-D290 doi: 10.1093/nar/gkj163

2005

SOAP-based services provided by the European Bioinformatics Institute
Pillai, S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., et al.
Nucleic Acids Research. Volume 33, Issue Web Server issue, (2005), p.W25-W28 doi: 10.1093/nar/gki491
E-MSD: an integrated data resource for bioinformatics
Velankar, S., McNeil P., Mittard-Runte V., Suarez A., Barrell D., Apweiler R., and Henrick K.
Nucleic Acids Research. Volume 33, Issue Database issue, (2005), p.D262-D265 doi: 10.1093/nar/gki058

2004

E-MSD: an integrated data resource for bioinformatics
Oldfield, T. J., Golovin A., Tate J. G., Velankar S., Barton G. J., Boutselakis H., Dimitropoulos D., Fillon J., Hussain A., Ionides J.M.C., et al.
Nucleic Acids Research. Volume 32, Issue Database issue, (2004), p.D211-D216. doi: 10.1093/nar/gkh078
Unconventional interactions between water and heterocyclic nitrogens in protein structures
Stollar, E.J., Gelpi J.L., Velankar S., Golovin A., Orozco M., and Luisi B.F.
Proteins. Volume 57, Issue 1, (2004), p.1-8 doi: 10.1002/prot.20216

2003

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database
Boutselakis, H., Dimitropoulos D., Fillon J., Henrick K., Hussain A., Ionides J., John M., Keller P.A., Krissinel E., McNeil P., et al.
Nucleic Acids Research. Volume 31, Issue 1, (2003), p.458-462 doi: 10.1093/nar/gkg065

Services

PDBe
SIFTS

Team members

John Berrisford
Matthew Conroy
Jose Dana
Swanand Gore
Gaurav Sahni
Sanchayita Sen
Glen van Ginkel