Publications

2018

Structural biology data archiving - where we are and what lies ahead.
Kleywegt GJ, Velankar S, Patwardhan A.
FEBS letters Volume 592 (2018) p.2153-2167
DOI: 10.1002/1873-3468.13086

Worldwide Protein Data Bank validation information: usage and trends.
Smart OS, Horský V, Gore S, Svobodová Vařeková R, Bendová V, Kleywegt GJ, Velankar S.
Acta crystallographica. Section D, Structural biology Volume 74 (2018) p.237-244
DOI: 10.1107/S2059798318003303

Validation of ligands in macromolecular structures determined by X-ray crystallography.
Smart OS, Horský V, Gore S, Svobodová Vařeková R, Bendová V, Kleywegt GJ, Velankar S.
Acta crystallographica. Section D, Structural biology Volume 74 (2018) p.228-236
DOI: 10.1107/S2059798318002541

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK.
Database : the journal of biological databases and curation Volume 2018 (2018)
DOI: 10.1093/database/bay002

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S.
Nucleic acids research Volume 46 (2018) p.D486-D492
DOI: 10.1093/nar/gkx1070

The challenge of modeling protein assemblies: the CASP12-CAPRI experiment.
Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ.
Proteins Volume 86 Suppl 1 (2018) p.257-273
DOI: 10.1002/prot.25419

2017

Validation of Structures in the Protein Data Bank.
Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ.
Structure (London, England : 1993) Volume 25 (2017) p.1916-1927
DOI: 10.1016/j.str.2017.10.009

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.
Sehnal D, Deshpande M, Vařeková RS, Mir S, Berka K, Midlik A, Pravda L, Velankar S, Koča J.
Nature methods Volume 14 (2017) p.1121-1122
DOI: 10.1038/nmeth.4499

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.
Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J.
Structure (London, England : 1993) Volume 25 (2017) p.1317-1318
DOI: 10.1016/j.str.2017.08.001

Building bridges between cellular and molecular structural biology.
Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ.
eLife Volume 6 (2017)
DOI: 10.7554/eLife.25835

SDM: a server for predicting effects of mutations on protein stability.
Pandurangan AP, Ochoa-Montaño B, Ascher DB, Blundell TL.
Nucleic acids research Volume 45 (2017) p.W229-W235
DOI: 10.1093/nar/gkx439

Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M.
Journal of structural biology Volume 199 (2017) p.12-26
DOI: 10.1016/j.jsb.2017.05.007

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.
Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK.
Structure (London, England : 1993) Volume 25 (2017) p.536-545
DOI: 10.1016/j.str.2017.01.004

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.
Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.
Methods in molecular biology (Clifton, N.J.) Volume 1607 (2017) p.627-641
DOI: 10.1007/978-1-4939-7000-1_26

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.
Lensink MF, Velankar S, Wodak SJ.
Proteins Volume 85 (2017) p.359-377
DOI: 10.1002/prot.25215

2016

Resolution of ab initio shapes determined from small-angle scattering.
Tuukkanen AT, Kleywegt GJ, Svergun DI.
IUCrJ Volume 3 (2016) p.440-447
DOI: 10.1107/S2052252516016018

Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
Speranzini V, Rotili D, Ciossani G, Pilotto S, Marrocco B, Forgione M, Lucidi A, Forneris F, Mehdipour P, Velankar S, Mai A, Mattevi A.
Science advances Volume 2 (2016) p.e1601017
DOI: 10.1126/sciadv.1601017

The archiving and dissemination of biological structure data.
Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.
Current opinion in structural biology Volume 40 (2016) p.17-22
DOI: 10.1016/j.sbi.2016.06.018

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.
Proteins Volume 84 Suppl 1 (2016) p.323-348
DOI: 10.1002/prot.25007

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.
Structure (London, England : 1993) Volume 24 (2016) p.502-508
DOI: 10.1016/j.str.2016.02.017

EMPIAR: a public archive for raw electron microscopy image data.
Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A.
Nature methods Volume 13 (2016) p.387-388
DOI: 10.1038/nmeth.3806

Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
Bousfield D, McEntyre J, Velankar S, Papadatos G, Bateman A, Cochrane G, Kim JH, Graef F, Vartak V, Alako B, Blomberg N.
F1000Research Volume 5 (2016)
DOI: 10.12688/f1000research.7911.1

Web-based volume slicer for 3D electron-microscopy data from EMDB.
Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A.
Journal of structural biology Volume 194 (2016) p.164-170
DOI: 10.1016/j.jsb.2016.02.012

Highly sensitive and ultrafast read mapping for RNA-seq analysis.
Medina I, Tárraga J, Martínez H, Barrachina S, Castillo MI, Paschall J, Salavert-Torres J, Blanquer-Espert I, Hernández-García V, Quintana-Ortí ES, Dopazo J.
DNA research : an international journal for rapid publication of reports on genes and genomes Volume 23 (2016) p.93-100
DOI: 10.1093/dnares/dsv039

EMDataBank unified data resource for 3DEM.
Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W.
Nucleic acids research Volume 44 (2016) p.D396-403
DOI: 10.1093/nar/gkv1126

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ.
Nucleic acids research Volume 44 (2016) p.D385-95
DOI: 10.1093/nar/gkv1047

2015

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.
Structure (London, England : 1993) Volume 23 (2015) p.1156-1167
DOI: 10.1016/j.str.2015.05.013

NMR Exchange Format: a unified and open standard for representation of NMR restraint data.
Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW.
Nature structural & molecular biology Volume 22 (2015) p.433-434
DOI: 10.1038/nsmb.3041

Fast inexact mapping using advanced tree exploration on backward search methods.
Salavert J, Tomás A, Tárraga J, Medina I, Dopazo J, Blanquer I.
BMC bioinformatics Volume 16 (2015) p.18
DOI: 10.1186/s12859-014-0438-3

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.
Westbrook JD, Shao C, Feng Z, Zhuravleva M, Velankar S, Young J.
Bioinformatics (Oxford, England) Volume 31 (2015) p.1274-1278
DOI: 10.1093/bioinformatics/btu789

Genome3D: exploiting structure to help users understand their sequences.
Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, Murzin AG, Ochoa-Montaño B, Oates ME, Punta M, Rackham OJ, Stahlhacke J, Sternberg MJ, Velankar S, Orengo C.
Nucleic acids research Volume 43 (2015) p.D382-6
DOI: 10.1093/nar/gku973

The complex portal--an encyclopaedia of macromolecular complexes.
Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S.
Nucleic Acids Research Volume 43 (2015) p.D479-84
DOI: 10.1093/nar/gku975

2014

Small molecule annotation for the Protein Data Bank.
Sen S, Young J, Berrisford JM, Chen M, Conroy MJ, Dutta S, Di Costanzo L, Gao G, Ghosh S, Hudson BP, Igarashi R, Kengaku Y, Liang Y, Peisach E, Persikova I, Mukhopadhyay A, Narayanan BC, Sahni G, Sato J, Sekharan M, Shao C, Tan L, Zhuravleva MA.
Database : the journal of biological databases and curation Volume 2014 (2014) p.bau116
DOI: 10.1093/database/bau116

A 3D cellular context for the macromolecular world.
Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ.
Nature structural & molecular biology Volume 21 (2014) p.841-845
DOI: 10.1038/nsmb.2897

Response to On prompt update of literature references in the Protein Data Bank.
Berman HM, Burley SK, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 70 (2014) p.2780
DOI: 10.1107/S1399004714020513

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.
Tárraga J, Arnau V, Martínez H, Moreno R, Cazorla D, Salavert-Torres J, Blanquer-Espert I, Dopazo J, Medina I.
Bioinformatics (Oxford, England) Volume 30 (2014) p.3396-3398
DOI: 10.1093/bioinformatics/btu553

The Protein Data Bank archive as an open data resource.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Journal of computer-aided molecular design Volume 28 (2014) p.1009-1014
DOI: 10.1007/s10822-014-9770-y

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.
Dutta S, Dimitropoulos D, Feng Z, Persikova I, Sen S, Shao C, Westbrook J, Young J, Zhuravleva MA, Kleywegt GJ, Berman HM.
Biopolymers Volume 101 (2014) p.659-668
DOI: 10.1002/bip.22434

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, 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, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ.
Nucleic acids research Volume 42 (2014) p.D285-91
DOI: 10.1093/nar/gkt1180

An overview of tools for the validation of protein NMR structures.
Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A.
Journal of biomolecular NMR Volume 58 (2014) p.259-285
DOI: 10.1007/s10858-013-9750-x

2013

Comment on on the propagation of errors by Jaskolski (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2297
DOI: 10.1107/S090744491302917X

Comment on timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013).
Berman H, Kleywegt GJ, Nakamura H, Markley JL.
Acta crystallographica. Section D, Biological crystallography Volume 69 (2013) p.2296
DOI: 10.1107/S0907444913029168

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.
Lagerstedt I, Moore WJ, Patwardhan A, Sanz-García E, Best C, Swedlow JR, Kleywegt GJ.
Journal of structural biology Volume 184 (2013) p.173-181
DOI: 10.1016/j.jsb.2013.09.021

How community has shaped the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Structure (London, England : 1993) Volume 21 (2013) p.1485-1491
DOI: 10.1016/j.str.2013.07.010

Recommendations of the wwPDB NMR Validation Task Force.
Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL.
Structure (London, England : 1993) Volume 21 (2013) p.1563-1570
DOI: 10.1016/j.str.2013.07.021

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

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.
Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM.
Structure (London, England : 1993) Volume 21 (2013) p.875-881
DOI: 10.1016/j.str.2013.04.020

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 crystallographica. Section D, Biological crystallography Volume 69 (2013) p.710-721
DOI: 10.1107/S0907444913001157

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 (Oxford, England) Volume 29 (2013) p.1103-1104
DOI: 10.1093/bioinformatics/btt100

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ.
Proteins Volume 81 (2013) p.583-591
DOI: 10.1002/prot.24213

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.
Journal of cheminformatics Volume 5 (2013) p.3
DOI: 10.1186/1758-2946-5-3

Emdatabank: Unified Data Resource for 3DEM
Catherine Lawson, Ardan Patwardhan, Grigore D Pintilie, Eduardo Sanz Garcia, Ingvar Lagerstedt, Matthew L Baker, Raul Sala, Steven J Ludtke, Helen M Berman, Gerard Kleywegt, Wah Chiu.
Biophysical journal Volume 104 (2013) p.351a
DOI: 10.1016/j.bpj.2012.11.1950

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 research Volume 41 (2013) p.D499-507
DOI: 10.1093/nar/gks1266

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 research Volume 41 (2013) p.D483-9
DOI: 10.1093/nar/gks1258

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 research Volume 41 (2013) p.D773-80
DOI: 10.1093/nar/gks1112

The future of the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Biopolymers Volume 99 (2013) p.218-222
DOI: 10.1002/bip.22132

2012

Data management challenges in three-dimensional EM.
Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ.
Nature structural & molecular biology Volume 19 (2012) p.1203-1207
DOI: 10.1038/nsmb.2426

The 2010 cryo-EM modeling challenge.
Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W.
Biopolymers Volume 97 (2012) p.651-654
DOI: 10.1002/bip.22081

Implementing an X-ray validation pipeline for the Protein Data Bank.
Gore S, Velankar S, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 68 (2012) p.478-483
DOI: 10.1107/S0907444911050359

The Protein Data Bank at 40: reflecting on the past to prepare for the future.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL.
Structure (London, England : 1993) Volume 20 (2012) p.391-396
DOI: 10.1016/j.str.2012.01.010

OMERO: flexible, model-driven data management for experimental biology.
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR.
Nature methods Volume 9 (2012) p.245-253
DOI: 10.1038/nmeth.1896

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 crystallographica. Section F, Structural biology and crystallization communications Volume 68 (2012) p.253-258
DOI: 10.1107/S1744309112002618

Outcome of the first electron microscopy validation task force meeting.
Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL.
Structure (London, England : 1993) Volume 20 (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 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 research Volume 40 (2012) p.D445-52
DOI: 10.1093/nar/gkr998

2011

A new generation of crystallographic validation tools for the protein data bank.
Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH.
Structure (London, England : 1993) Volume 19 (2011) p.1395-1412
DOI: 10.1016/j.str.2011.08.006

Asymmetric synthesis and conformational analysis by NMR spectroscopy and MD of Aba- and α-MeAba-containing dermorphin analogues.
Vandormael B, De Wachter R, Martins JC, Hendrickx PM, Keresztes A, Ballet S, Mallareddy JR, Tóth F, Tóth G, Tourwé D.
ChemMedChem Volume 6 (2011) p.2035-2047
DOI: 10.1002/cmdc.201100314

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.
Nature methods Volume 8 (2011) p.528-529
DOI: 10.1038/nmeth.1637

The Protein Data Bank in Europe (PDBe): bringing structure to biology.
Velankar S, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 67 (2011) p.324-330
DOI: 10.1107/S090744491004117X

Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines.
Ludtke SJ, Lawson CL, Kleywegt GJ, Berman HM, Chiu W.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2011) p.369-373

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 research Volume 39 (2011) p.D402-10
DOI: 10.1093/nar/gkq985

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 research Volume 39 (2011) p.D456-64
DOI: 10.1093/nar/gkq880

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.
Journal of biomolecular NMR Volume 48 (2010) p.85-92
DOI: 10.1007/s10858-010-9439-3

Towards Proteome-Wide Interaction Models Using the Proteochemometrics Approach.
Strömbergsson H, Lapins M, Kleywegt GJ, Wikberg JE.
Molecular informatics Volume 29 (2010) p.499-508
DOI: 10.1002/minf.201000052

Assignment and conformational investigation of asymmetric phenylindenylidene ruthenium complexes bearing N,O-bidentate ligands.
Hendrickx PM, Drozdzak R, Verpoort F, Martins JC.
Magnetic resonance in chemistry : MRC Volume 48 (2010) p.443-449
DOI: 10.1002/mrc.2599

Integration of chemical information with protein sequences and 3D structures.
Golovin A, Henrick K, Kleywegt G.
Journal of cheminformatics Volume 2 (2010) p.O17-O17
DOI: 10.1186/1758-2946-2-S1-O17

Practical application of bioinformatics by the multidisciplinary VIZIER consortium.
Gorbalenya AE, Lieutaud P, Harris MR, Coutard B, Canard B, Kleywegt GJ, Kravchenko AA, Samborskiy DV, Sidorov IA, Leontovich AM, Jones TA.
Antiviral research Volume 87 (2010) p.95-110
DOI: 10.1016/j.antiviral.2010.02.005

The use of time-averaged 3JHH restrained molecular dynamics (tar-MD) simulations for the conformational analysis of five-membered ring systems: methodology and applications.
Hendrickx PM, Corzana F, Depraetere S, Tourwé DA, Augustyns K, Martins JC.
Journal of computational chemistry Volume 31 (2010) p.561-572
DOI: 10.1002/jcc.21345

Safeguarding the integrity of protein archive.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL, Burley SK.
Nature Volume 463 (2010) p.425
DOI: 10.1038/463425c

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 research Volume 38 (2010) p.D308-17
DOI: 10.1093/nar/gkp916

2009

A chemogenomics view on protein-ligand spaces.
Strömbergsson H, Kleywegt GJ.
BMC bioinformatics Volume 10 Suppl 6 (2009) p.S13
DOI: 10.1186/1471-2105-10-S6-S13

On vital aid: the why, what and how of validation.
Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 65 (2009) p.134-139
DOI: 10.1107/S090744490900081X

Case-controlled structure validation.
Read RJ, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 65 (2009) p.140-147
DOI: 10.1107/S0907444908041085

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 research Volume 36 (2008) p.D426-33
DOI: 10.1093/nar/gkm937

2006

Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP.
Sen S, Krishnakumar A, McClead J, Johnson MK, Seefeldt LC, Szilagyi RK, Peters JW.
Journal of inorganic biochemistry Volume 100 (2006) p.1041-1052
DOI: 10.1016/j.jinorgbio.2006.02.016

E-MSD: improving data deposition and structure quality.
Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S.
Nucleic acids research Volume 34 (2006) p.D287-90
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, Stoehr P, Lopez R.
Nucleic acids research 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 research 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

E-MSD: an integrated data resource for bioinformatics.
Golovin A, Oldfield TJ, Tate JG, Velankar S, Barton GJ, Boutselakis H, Dimitropoulos D, Fillon J, Hussain A, Ionides JM, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Pajon A, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan GJ, Tagari M, Tromm S, Vranken W, Henrick K.
Nucleic acids research Volume 32 (2004) p.D211-6
DOI: 10.1093/nar/gkh078

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 research Volume 31 (2003) p.458-462
DOI: 10.1093/nar/gkg065