Publications

2020

Interaction between the scaffold proteins CBP by IQGAP1 provides an interface between gene expression and cytoskeletal activity.
Kosol S, Contreras-Martos S, Piai A, Varadi M, Lazar T, Bekesi A, Lebrun P, Felli IC, Pierattelli R, Tompa P.
Scientific reports Volume 10 (2020) p.5753
DOI: 10.1038/s41598-020-62069-w

Structures of Type III Secretion System Needle Filaments.
Habenstein B, El Mammeri N, Tolchard J, Lamon G, Tawani A, Berbon M, Loquet A.
Current topics in microbiology and immunology (2020)
DOI: 10.1007/82_2019_192

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.
Drysdale R, Cook CE, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E, Gruhl F, Haas J, Lanfear J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Venkatesan A, Elixir Core Data Resource Forum , Blomberg N, Durinx C, McEntyre J.
Bioinformatics (Oxford, England) Volume 36 (2020) p.2636-2642
DOI: 10.1093/bioinformatics/btz959

PDBe-KB: a community-driven resource for structural and functional annotations.
PDBe-KB consortium.
Nucleic acids research Volume 48 (2020) p.D344-D353
DOI: 10.1093/nar/gkz853

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.
Sillitoe I, Andreeva A, Blundell TL, Buchan DWA, Finn RD, Gough J, Jones D, Kelley LA, Paysan-Lafosse T, Lam SD, Murzin AG, Pandurangan AP, Salazar GA, Skwark MJ, Sternberg MJE, Velankar S, Orengo C.
Nucleic acids research Volume 48 (2020) p.D314-D319
DOI: 10.1093/nar/gkz967

PDBe: improved findability of macromolecular structure data in the PDB.
Armstrong DR, Berrisford JM, Conroy MJ, Gutmanas A, Anyango S, Choudhary P, Clark AR, Dana JM, Deshpande M, Dunlop R, Gane P, Gáborová R, Gupta D, Haslam P, Koča J, Mak L, Mir S, Mukhopadhyay A, Nadzirin N, Nair S, Paysan-Lafosse T, Pravda L, Sehnal D, Salih O, Smart O, Tolchard J, Varadi M, Svobodova-Vařeková R, Zaki H, Kleywegt GJ, Velankar S.
Nucleic acids research Volume 48 (2020) p.D335-D343
DOI: 10.1093/nar/gkz990

2019

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A.
Structure (London, England : 1993) Volume 27 (2019) p.1745-1759
DOI: 10.1016/j.str.2019.11.002

Automatic annotation of protein residues in published papers.
Firth R, Talo F, Venkatesan A, Mukhopadhyay A, McEntyre J, Velankar S, Morris C.
Acta crystallographica. Section F, Structural biology communications Volume 75 (2019) p.665-672
DOI: 10.1107/s2053230x1901210x

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ.
Proteins Volume 87 (2019) p.1200-1221
DOI: 10.1002/prot.25838

An intrinsically disordered proteins community for ELIXIR.
Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE.
F1000Research Volume 8 (2019)
DOI: 10.12688/f1000research.20136.1

Smad7 Binds Differently to Individual and Tandem WW3 and WW4 Domains of WWP2 Ubiquitin Ligase Isoforms.
Wahl LC, Watt JE, Yim HTT, De Bourcier D, Tolchard J, Soond SM, Blumenschein TMA, Chantry A.
International journal of molecular sciences Volume 20 (2019)
DOI: 10.3390/ijms20194682

Finding enzyme cofactors in Protein Data Bank.
Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S.
Bioinformatics (Oxford, England) Volume 35 (2019) p.3510-3511
DOI: 10.1093/bioinformatics/btz115

Assembly of B4GALT1/ST6GAL1 heteromers in the Golgi membranes involves lateral interactions via highly charged surface domains.
Khoder-Agha F, Harrus D, Brysbaert G, Lensink MF, Harduin-Lepers A, Glumoff T, Kellokumpu S.
The Journal of biological chemistry Volume 294 (2019) p.14383-14393
DOI: 10.1074/jbc.ra119.009539

A polymorphic helix of a Salmonella needle protein relays signals defining distinct steps in type III secretion.
Guo EZ, Desrosiers DC, Zalesak J, Tolchard J, Berbon M, Habenstein B, Marlovits T, Loquet A, Galán JE.
PLoS biology Volume 17 (2019) p.e3000351
DOI: 10.1371/journal.pbio.3000351

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).
Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY.
Acta crystallographica. Section D, Structural biology Volume 75 (2019) p.451-454
DOI: 10.1107/s2059798319004522

Structural and Functional Characterization of the Type Three Secretion System (T3SS) Needle of Pseudomonas aeruginosa.
Lombardi C, Tolchard J, Bouillot S, Signor L, Gebus C, Liebl D, Fenel D, Teulon JM, Brock J, Habenstein B, Pellequer JL, Faudry E, Loquet A, Attrée I, Dessen A, Job V.
Frontiers in microbiology Volume 10 (2019) p.573
DOI: 10.3389/fmicb.2019.00573

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana JM, Gutmanas A, Tyagi N, Qi G, O'Donovan C, Martin M, Velankar S.
Nucleic acids research Volume 47 (2019) p.D482-D489
DOI: 10.1093/nar/gky1114

Protein Data Bank: the single global archive for 3D macromolecular structure data.
wwPDB consortium.
Nucleic acids research Volume 47 (2019) p.D520-D528
DOI: 10.1093/nar/gky949

2018

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).
Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vareková R, Koca J, Otyepka M.
Nucleic acids research Volume 46 (2018) p.W368-W373
DOI: 10.1093/nar/gky309

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

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 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

AmyPro: a database of proteins with validated amyloidogenic regions.
Varadi M, De Baets G, Vranken WF, Tompa P, Pancsa R.
Nucleic acids research Volume 46 (2018) p.D387-D392
DOI: 10.1093/nar/gkx950

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

ChannelsDB: database of biomacromolecular tunnels and pores.
Pravda L, Sehnal D, Svobodová Vareková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koca J.
Nucleic acids research Volume 46 (2018) p.D399-D405
DOI: 10.1093/nar/gkx868

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

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

PDBsum: Structural summaries of PDB entries.
Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM.
Protein science : a publication of the Protein Society Volume 27 (2018) p.129-134
DOI: 10.1002/pro.3289

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

Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP.
Contreras-Martos S, Piai A, Kosol S, Varadi M, Bekesi A, Lebrun P, Volkov AN, Gevaert K, Pierattelli R, Felli IC, Tompa P.
Scientific reports Volume 7 (2017) p.4676
DOI: 10.1038/s41598-017-04611-x

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

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

Synthesis of Chlorophyll-Binding Proteins in a Fully Segregated Δycf54 Strain of the Cyanobacterium Synechocystis PCC 6803.
Hollingshead S, Kopečná J, Armstrong DR, Bučinská L, Jackson PJ, Chen GE, Dickman MJ, Williamson MP, Sobotka R, Hunter CN.
Frontiers in plant science Volume 7 (2016) p.292
DOI: 10.3389/fpls.2016.00292

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

Structure of bacterial respiratory complex I.
Berrisford JM, Baradaran R, Sazanov LA.
Biochimica et biophysica acta Volume 1857 (2016) p.892-901
DOI: 10.1016/j.bbabio.2016.01.012

Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy.
Piai A, Calçada EO, Tarenzi T, Grande AD, Varadi M, Tompa P, Felli IC, Pierattelli R.
Biophysical journal Volume 110 (2016) p.372-381
DOI: 10.1016/j.bpj.2015.11.3516

Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability.
Pancsa R, Varadi M, Tompa P, Vranken WF.
Nucleic acids research Volume 44 (2016) p.D429-34
DOI: 10.1093/nar/gkv1185

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

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.
Varadi M, Zsolyomi F, Guharoy M, Tompa P.
PloS one Volume 10 (2015) p.e0139731
DOI: 10.1371/journal.pone.0139731

Computational approaches for inferring the functions of intrinsically disordered proteins.
Varadi M, Vranken W, Guharoy M, Tompa P.
Frontiers in molecular biosciences Volume 2 (2015) p.45
DOI: 10.3389/fmolb.2015.00045

Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.
Mak L, Marcus D, Howlett A, Yarova G, Duchateau G, Klaffke W, Bender A, Glen RC.
Journal of cheminformatics Volume 7 (2015) p.31
DOI: 10.1186/s13321-015-0083-5

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

DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder.
Varadi M, Guharoy M, Zsolyomi F, Tompa P.
BMC bioinformatics Volume 16 (2015) p.153
DOI: 10.1186/s12859-015-0592-2

A contribution to the rational design of Ru(CO)3Cl2L complexes for in vivo delivery of CO.
Seixas JD, Santos MF, Mukhopadhyay A, Coelho AC, Reis PM, Veiros LF, Marques AR, Penacho N, Gonçalves AM, Romão MJ, Bernardes GJ, Santos-Silva T, Romão CC.
Dalton transactions (Cambridge, England : 2003) Volume 44 (2015) p.5058-5075
DOI: 10.1039/c4dt02966f

Diverse phenotypic consequences of mutations affecting the C-terminus of FLNA.
van Kogelenberg M, Clark AR, Jenkins Z, Morgan T, Anandan A, Sawyer GM, Edwards M, Dudding T, Homfray T, Castle B, Tolmie J, Stewart F, Kivuva E, Pilz DT, Gabbett M, Sutherland-Smith AJ, Robertson SP.
Journal of molecular medicine (Berlin, Germany) Volume 93 (2015) p.773-782
DOI: 10.1007/s00109-015-1261-7

The Protein Ensemble Database.
Varadi M, Tompa P.
Advances in experimental medicine and biology Volume 870 (2015) p.335-349
DOI: 10.1007/978-3-319-20164-1_11

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

Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.
Lemak A, Wu B, Yee A, Houliston S, Lee HW, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, Arrowsmith CH.
Structure (London, England : 1993) Volume 22 (2014) p.1862-1874
DOI: 10.1016/j.str.2014.09.013

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

The ChEMBL bioactivity database: an update.
Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP.
Nucleic acids research Volume 42 (2014) p.D1083-90
DOI: 10.1093/nar/gkt1031

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

A long road towards the structure of respiratory complex I, a giant molecular proton pump.
Sazanov LA, Baradaran R, Efremov RG, Berrisford JM, Minhas G.
Biochemical Society transactions Volume 41 (2013) p.1265-1271
DOI: 10.1042/bst20130193

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

Characterization of a versatile organometallic pro-drug (CORM) for experimental CO based therapeutics.
Seixas JD, Mukhopadhyay A, Santos-Silva T, Otterbein LE, Gallo DJ, Rodrigues SS, Guerreiro BH, Gonçalves AM, Penacho N, Marques AR, Coelho AC, Reis PM, Romão MJ, Romão CC.
Dalton transactions (Cambridge, England : 2003) Volume 42 (2013) p.5985-5998
DOI: 10.1039/c2dt32174b

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

Crystal structure of the entire respiratory complex I.
Baradaran R, Berrisford JM, Minhas GS, Sazanov LA.
Nature Volume 494 (2013) p.443-448
DOI: 10.1038/nature11871

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

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

2012

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 bacterial stressosome: a modular system that has been adapted to control secondary messenger signaling.
Quin MB, Berrisford JM, Newman JA, Baslé A, Lewis RJ, Marles-Wright J.
Structure (London, England : 1993) Volume 20 (2012) p.350-363
DOI: 10.1016/j.str.2012.01.003

Blind testing of routine, fully automated determination of protein structures from NMR data.
Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, Jaravine V, Jonker HR, Kennedy MA, Lange OF, Liu G, Malliavin TE, Mani R, Mao B, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, Vries Sd, Vuister GW, Wu B, Yang Y, Bonvin AM.
Structure (London, England : 1993) Volume 20 (2012) p.227-236
DOI: 10.1016/j.str.2012.01.002

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

SABIO-RK--database for biochemical reaction kinetics.
Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauer-Danzwith H, Mir S, Krebs O, Bittkowski M, Wetsch E, Rojas I, Müller W.
Nucleic acids research Volume 40 (2012) p.D790-6
DOI: 10.1093/nar/gkr1046

2011

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

A novel strategy for NMR resonance assignment and protein structure determination.
Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH.
Journal of biomolecular NMR Volume 49 (2011) p.27-38
DOI: 10.1007/s10858-010-9458-0

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

Enzyme kinetics informatics: from instrument to browser.
Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Müller W, Paton NW, Rojas I.
The FEBS journal Volume 277 (2010) p.3769-3779
DOI: 10.1111/j.1742-4658.2010.07778.x

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

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

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