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.

ORCID iD: 0000-0002-8439-5964

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

2014

PDBe: Protein Data Bank in Europe.
Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ.
Nucleic Acids Res Volume 42 (2014) p.d285-91
DOI: 10.1093/nar/gkt1180

2013

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, Overington JP.
J Cheminform Volume 5 (2013) p.3
DOI: 10.1186/1758-2946-5-3

BioJS: an open source JavaScript framework for biological data visualization.
Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.
Bioinformatics Volume 29 (2013) p.1103-1104
DOI: 10.1093/bioinformatics/btt100

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C.
Nucleic Acids Res Volume 41 (2013) p.d499-507
DOI: 10.1093/nar/gks1266

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.
Proteins Volume 81 (2013) p.1980-1987
DOI: 10.1002/prot.24356

The role of structural bioinformatics resources in the era of integrative structural biology.
Gutmanas A, Oldfield TJ, Patwardhan A, Sen S, Velankar S, Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 69 (2013) p.710-721
DOI: 10.1107/s0907444913001157

The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.
Nucleic Acids Res Volume 41 (2013) p.d773-80
DOI: 10.1093/nar/gks1112

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource.
Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ.
Nucleic Acids Res Volume 41 (2013) p.d483-9
DOI: 10.1093/nar/gks1258

2012

Implementing an X-ray validation pipeline for the Protein Data Bank.
Gore S, Velankar S, Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 68 (2012) p.478-483
DOI: 10.1107/s0907444911050359

PDBe: Protein Data Bank in Europe.
Velankar S, Alhroub Y, Best C, Caboche S, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Heuson E, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley R, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ.
Nucleic Acids Res Volume 40 (2012) p.d445-52
DOI: 10.1093/nar/gkr998

On the need for an international effort to capture, share and use crystallization screening data.
Newman J, Bolton EE, Müller-Dieckmann J, Fazio VJ, Gallagher DT, Lovell D, Luft JR, Peat TS, Ratcliffe D, Sayle RA, Snell EH, Taylor K, Vallotton P, Velanker S, von Delft F.
Acta Crystallogr Sect F Struct Biol Cryst Commun Volume 68 (2012) p.253-258
DOI: 10.1107/s1744309112002618

2011

The Protein Data Bank in Europe (PDBe): bringing structure to biology.
Velankar S, Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 67 (2011) p.324-330
DOI: 10.1107/s090744491004117x

EMDataBank.org: unified data resource for CryoEM.
Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W.
Nucleic Acids Res Volume 39 (2011) p.d456-64
DOI: 10.1093/nar/gkq880

PDBe: Protein Data Bank in Europe.
Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ.
Nucleic Acids Res Volume 39 (2011) p.d402-10
DOI: 10.1093/nar/gkq985

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.
Nat Methods Volume 8 (2011) p.528-529
DOI: 10.1038/nmeth.1637

2010

Straightforward and complete deposition of NMR data to the PDBe.
Penkett CJ, van Ginkel G, Velankar S, Swaminathan J, Ulrich EL, Mading S, Stevens TJ, Fogh RH, Gutmanas A, Kleywegt GJ, Henrick K, Vranken WF.
J Biomol NMR Volume 48 (2010) p.85-92
DOI: 10.1007/s10858-010-9439-3

PDBe: Protein Data Bank in Europe.
Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ.
Nucleic Acids Res Volume 38 (2010) p.d308-17
DOI: 10.1093/nar/gkp916

2008

Remediation of the protein data bank archive.
Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM.
Nucleic Acids Res Volume 36 (2008) p.d426-33
DOI: 10.1093/nar/gkm937

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, Stoehr P, Lopez R.
Nucleic Acids Res Volume 33 (2005) p.w25-8
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, Henrick K.
Nucleic Acids Res Volume 33 (2005) p.d262-5
DOI: 10.1093/nar/gki058

2004

Unconventional interactions between water and heterocyclic nitrogens in protein structures.
Stollar EJ, Gelpí JL, Velankar S, Golovin A, Orozco M, Luisi BF.
Proteins Volume 57 (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, Golovin A, Henrick K, Hussain A, Ionides J, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Oldfield T, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan J, Tagari M, Tate J, Tromm S, Velankar S, Vranken W.
Nucleic Acids Res Volume 31 (2003) p.458-462
DOI: 10.1093/nar/gkg065

1999

Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism.
Velankar SS, Soultanas P, Dillingham MS, Subramanya HS, Wigley DB.
Cell Volume 97 (1999) p.75-84
DOI: 10.1016/s0092-8674(00)80716-3

Disulfide engineering at the dimer interface of Lactobacillus casei thymidylate synthase: crystal structure of the T155C/E188C/C244T mutant.
Velanker SS, Gokhale RS, Ray SS, Gopal B, Parthasarathy S, Santi DV, Balaram P, Murthy MR.
Protein Sci Volume 8 (1999) p.930-933
DOI: 10.1110/ps.8.4.930

DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase.
Soultanas P, Dillingham MS, Velankar SS, Wigley DB.
J Mol Biol Volume 290 (1999) p.137-148
DOI: 10.1006/jmbi.1999.2873

1997

Triosephosphate isomerase from Plasmodium falciparum: the crystal structure provides insights into antimalarial drug design.
Velanker SS, Ray SS, Gokhale RS, Suma S, Balaram H, Balaram P, Murthy MR.
Structure Volume 5 (1997) p.751-761
DOI: 10.1016/s0969-2126(97)00230-x

Services

Team members

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