Harnessing the 3D-Beacons Network: A Comprehensive Guide to Accessing and Displaying Protein Structure Data.

Magaña P, Nair S, Varadi M, Velankar S.

Curr Protoc, 2024

doi:10.1002/cpz1.1047.

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.

Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A.

J Mol Biol, 2024

doi:10.1016/j.jmb.2024.168546.

Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.

Baskaran K, Ploskon E, Tejero R, Yokochi M, Harrus D, Liang Y, Peisach E, Persikova I, Ramelot TA, Sekharan M, Tolchard J, Westbrook JD, Bardiaux B, Schwieters CD, Patwardhan A, Velankar S, Burley SK, Kurisu G, Hoch JC, Montelione GT, Vuister GW, Young JY.

Structure, 2024

doi:10.1016/j.str.2024.02.011.

Human-in-the-loop approach to identify functionally important residues of proteins from literature

Vollmar M, Tirunagari S, Harrus D, Armstrong D, Gaborova R, Gupta D, Afonso MQL, Evans GL, Velankar S.

2024

doi:10.1101/2024.03.09.583700.

Community recommendations on cryoEM data archiving and validation.

Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S.

IUCrJ, 2024

doi:10.1107/s2052252524001246.

Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank

Baskaran K, Ploskon E, Tejero R, Yokochi M, Harrus D, Liang Y, Peisach E, Persikova I, Ramelot TA, Sekharan M, Tolchard J, Westbrook JD, Bardiaux B, Schwieters CD, Patwardhan A, Velankar S, Burley SK, Kurisu G, Hoch JC, Montelione GT, Vuister GW, Young JY.

2024

doi:10.1101/2024.01.15.575520.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.

Thakur M, Buniello A, Brooksbank C, Gurwitz KT, Hall M, Hartley M, Hulcoop DG, Leach AR, Marques D, Martin M, Mithani A, McDonagh EM, Mutasa-Gottgens E, Ochoa D, Perez-Riverol Y, Stephenson J, Varadi M, Velankar S, Vizcaino JA, Witham R, McEntyre J.

Nucleic Acids Res, 2024

doi:10.1093/nar/gkad1088.

EMDB-the Electron Microscopy Data Bank.

wwPDB Consortium .

Nucleic Acids Res, 2024

doi:10.1093/nar/gkad1019.

AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences.

Varadi M, Bertoni D, Magana P, Paramval U, Pidruchna I, Radhakrishnan M, Tsenkov M, Nair S, Mirdita M, Yeo J, Kovalevskiy O, Tunyasuvunakool K, Laydon A, Žídek A, Tomlinson H, Hariharan D, Abrahamson J, Green T, Jumper J, Birney E, Steinegger M, Hassabis D, Velankar S.

Nucleic Acids Res, 2024

doi:10.1093/nar/gkad1011.

PDBImages: a command-line tool for automated macromolecular structure visualization.

Midlik A, Nair S, Anyango S, Deshpande M, Sehnal D, Varadi M, Velankar S.

Bioinformatics, 2023

doi:10.1093/bioinformatics/btad744.

CCPBioSim workshop: structural bioinformatics resources and tools for molecular dynamics simulations

Fegan S, Fraternali F, Gopalasingam P, Harris S, Johnson SP, Velankar S.

2023

doi:10.6019/tol.ccpbiosimworkshop-t.2023.00001.1.

Community recommendations on cryoEM data archiving and validation

Kleywegt GJ, Adams PD, Butcher SJ, Lawson C, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Morris K, Patwardhan A, Velankar S.

2023

doi:10.48550/arxiv.2311.17640.

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.

Kunnakkattu IR, Choudhary P, Pravda L, Nadzirin N, Smart OS, Yuan Q, Anyango S, Nair S, Varadi M, Velankar S.

J Cheminform, 2023

doi:10.1186/s13321-023-00786-w.

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data.

Appasamy SD, Berrisford J, Gaborova R, Nair S, Anyango S, Grudinin S, Deshpande M, Armstrong D, Pidruchna I, Ellaway JIJ, Leines GD, Gupta D, Harrus D, Varadi M, Velankar S.

Sci Data, 2023

doi:10.1038/s41597-023-02778-9.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ.

Proteins, 2023

doi:10.1002/prot.26609.

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank

Choudhary P, Feng Z, Berrisford J, Chao H, Ikegawa Y, Peisach E, Piehl DW, Smith J, Tanweer A, Varadi M, Westbrook JD, Young JY, Patwardhan A, Morris KL, Hoch JC, Kurisu G, Velankar S, Burley SK.

2023

doi:10.1101/2023.10.24.563739.

Challenges in bridging the gap between protein structure prediction and functional interpretation.

Varadi M, Tsenkov M, Velankar S.

Proteins, 2023

doi:10.1002/prot.26614.

Clustering predicted structures at the scale of the known protein universe.

Barrio-Hernandez I, Yeo J, Jänes J, Mirdita M, Gilchrist CLM, Wein T, Varadi M, Velankar S, Beltrao P, Steinegger M.

Nature, 2023

doi:10.1038/s41586-023-06510-w.

Structural biology: The transformational era.

Wodak SJ, Velankar S.

Proteomics, 2023

doi:10.1002/pmic.202200084.

Announcing the launch of Protein Data Bank China as an Associate Member of the Worldwide Protein Data Bank Partnership.

Xu W, Velankar S, Patwardhan A, Hoch JC, Burley SK, Kurisu G.

Acta Crystallogr D Struct Biol, 2023

doi:10.1107/s2059798323006381.

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank

Kunnakkattu IR, Choudhary P, Pravda L, Nadzirin N, Smart OS, Yuan Q, Anyango S, Nair S, Varadi M, Velankar S.

2023

doi:10.1101/2023.08.04.552003.

Automated Pipeline for Comparing Protein Conformational States in the PDB to AlphaFold2 Predictions

Ellaway JIJ, Anyango S, Nair S, Zaki HA, Nadzirin N, Powell HR, Gutmanas A, Varadi M, Velankar S.

2023

doi:10.1101/2023.07.13.545008.

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Lensink M, Brysbaert G, Raouraoua N, Bates P, Giulini M, Honorato RV, Noort Cv, Teixeira J, Bonvin AM, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy R, Wu T, Giri N, Quadir F, Chen C, Cheng J, Carpio CD, Ichiishi E, A LR, Fernández-Recio J, Harmalkar A, Chu L, Canner S, Smanta R, Gray J, Li H, Lin P, He J, Tao H, Huang S, Roel J, Jimenez-Garcia B, Christoffer C, J AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt J, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, S SN, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest J, Lee J, Pierce B, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, K KB, Lubecka E, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Giełdoń A, Liwo J, Samsonov S, Slusarz R, Zieba K, Sieradzan A, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovič K, Valančauskas L, Dapkūnas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qiu L, Xu X, Zou X, Velankar S, J SW.

2023

doi:10.22541/au.168888815.53957253/v1.

Challenges in Bridging the Gap Between Protein Structure Prediction and Functional Interpretation

Varadi M, Tsenkov M, Velankar S.

2023

doi:10.22541/au.168810664.47717663/v1.

The CCP4 suite: integrative software for macromolecular crystallography.

Agirre J, Atanasova M, Bagdonas H, Ballard CB, Baslé A, Beilsten-Edmands J, Borges RJ, Brown DG, Burgos-Mármol JJ, Berrisford JM, Bond PS, Caballero I, Catapano L, Chojnowski G, Cook AG, Cowtan KD, Croll TI, Debreczeni JÉ, Devenish NE, Dodson EJ, Drevon TR, Emsley P, Evans G, Evans PR, Fando M, Foadi J, Fuentes-Montero L, Garman EF, Gerstel M, Gildea RJ, Hatti K, Hekkelman ML, Heuser P, Hoh SW, Hough MA, Jenkins HT, Jiménez E, Joosten RP, Keegan RM, Keep N, Krissinel EB, Kolenko P, Kovalevskiy O, Lamzin VS, Lawson DM, Lebedev AA, Leslie AGW, Lohkamp B, Long F, Malý M, McCoy AJ, McNicholas SJ, Medina A, Millán C, Murray JW, Murshudov GN, Nicholls RA, Nicholls RA, Noble MEM, Oeffner R, Pannu NS, Parkhurst JM, Pearce N, Pereira J, Perrakis A, Powell HR, Read RJ, Rigden DJ, Rochira W, Sammito M, Sánchez Rodríguez F, Sheldrick GM, Shelley KL, Simkovic F, Simpkin AJ, Skubak P, Sobolev E, Steiner RA, Stevenson K, Tews I, Thomas JMH, Thorn A, Valls JT, Uski V, Usón I, Vagin A, Velankar S, Vollmar M, Walden H, Waterman D, Wilson KS, Winn MD, Winter G, Wojdyr M, Yamashita K.

Acta Crystallogr D Struct Biol, 2023

doi:10.1107/s2059798323003595.

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

Appasamy SD, Berrisford J, Gaborova R, Nair S, Anyango S, Grudinin S, Deshpande M, Armstrong D, Pidruchna I, Ellaway JIJ, Leines GD, Gupta D, Harrus D, Varadi M, Velankar S.

2023

doi:10.1101/2023.05.15.540692.

Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.

Choudhary P, Anyango S, Berrisford J, Tolchard J, Varadi M, Velankar S.

Sci Data, 2023

doi:10.1038/s41597-023-02101-6.

Clustering predicted structures at the scale of the known protein universe

Steinegger M, Beltrao P, Velankar S, Varadi M, Wein T, Gilchrist C, Mirdita M, Jänes J, Yeo J, Barrio-Hernandez I.

2023

doi:10.21203/rs.3.rs-2727632/v1.

Clustering predicted structures at the scale of the known protein universe

Barrio-Hernandez I, Yeo J, Jänes J, Wein T, Varadi M, Velankar S, Beltrao P, Steinegger M.

2023

doi:10.1101/2023.03.09.531927.

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.

Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD.

J Mol Biol, 2023

doi:10.1016/j.jmb.2023.168021.

The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors.

Varadi M, Bordin N, Orengo C, Velankar S.

Curr Opin Struct Biol, 2023

doi:10.1016/j.sbi.2023.102543.

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms.

Bordin N, Sillitoe I, Nallapareddy V, Rauer C, Lam SD, Waman VP, Sen N, Heinzinger M, Littmann M, Kim S, Velankar S, Steinegger M, Rost B, Orengo C.

Commun Biol, 2023

doi:10.1038/s42003-023-04488-9.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.

Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh EM, Orchard S, Papatheodorou I, Velankar S, Vizcaino JA, Witham R, Zdrazil B, McEntyre J.

Nucleic Acids Res, 2023

doi:10.1093/nar/gkac1098.

The impact of AlphaFold Protein Structure Database on the fields of life sciences.

Varadi M, Velankar S.

Proteomics, 2023

doi:10.1002/pmic.202200128.

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models

Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD.

2022

doi:10.1101/2022.12.06.518550.

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.

Varadi M, Nair S, Sillitoe I, Tauriello G, Anyango S, Bienert S, Borges C, Deshpande M, Green T, Hassabis D, Hatos A, Hegedus T, Hekkelman ML, Joosten R, Jumper J, Laydon A, Molodenskiy D, Piovesan D, Salladini E, Salzberg SL, Sommer MJ, Steinegger M, Suhajda E, Svergun D, Tenorio-Ku L, Tosatto S, Tunyasuvunakool K, Waterhouse AM, Žídek A, Schwede T, Orengo C, Velankar S.

Gigascience, 2022

doi:10.1093/gigascience/giac118.

A structural biology community assessment of AlphaFold2 applications.

Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P.

Nat Struct Mol Biol, 2022

doi:10.1038/s41594-022-00849-w.

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.

Varadi M, Anyango S, Appasamy SD, Armstrong D, Bage M, Berrisford J, Choudhary P, Bertoni D, Deshpande M, Leines GD, Ellaway J, Evans G, Gaborova R, Gupta D, Gutmanas A, Harrus D, Kleywegt GJ, Bueno WM, Nadzirin N, Nair S, Pravda L, Afonso MQL, Sehnal D, Tanweer A, Tolchard J, Abrams C, Dunlop R, Velankar S.

Protein Sci, 2022

doi:10.1002/pro.4439.

Unified access to up-to-date residue-level annotations from UniProt and other biological databases for PDB data via PDBx/mmCIF files

Choudhary P, Anyango S, Berrisford J, Varadi M, Tolchard J, Velankar S.

2022

doi:10.1101/2022.08.10.503473.

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Varadi M, Nair S, Sillitoe I, Tauriello G, Anyango S, Bienert S, Borges C, Deshpande M, Green T, Hassabis D, Hatos A, Hegedus T, Hekkelman ML, Joosten R, Jumper J, Laydon A, Molodenskiy D, Piovesan D, Salladini E, Salzberg SL, Sommer MJ, Steinegger M, Suhajda E, Svergun D, Tenorio-Ku L, Tosatto S, Tunyasuvunakool K, Waterhouse AM, Žídek A, Schwede T, Orengo C, Velankar S.

2022

doi:10.1101/2022.08.01.501973.

PDB ProtVista: A reusable and open-source sequence feature viewer

Deshpande M, Varadi M, Paysan-Lafosse T, Nair S, Piovesan D, Mir S, Gutmanas A, Tosatto SCE, Velankar S.

2022

doi:10.1101/2022.07.22.500790.

Whither structural biologists?

Kleywegt GJ, Velankar S.

IUCrJ, 2022

doi:10.1107/s2052252522005802.

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Bordin N, Sillitoe I, Nallapareddy V, Rauer C, Lam SD, Waman VP, Sen N, Heinzinger M, Littmann M, Kim S, Velankar S, Steinegger M, Rost B, Orengo C.

2022

doi:10.1101/2022.06.02.494367.

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.

Sen N, Anishchenko I, Bordin N, Sillitoe I, Velankar S, Baker D, Orengo C.

Brief Bioinform, 2022

doi:10.1093/bib/bbac187.

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.

Westbrook JD, Young JY, Shao C, Feng Z, Guranovic V, Lawson CL, Vallat B, Adams PD, Berrisford JM, Bricogne G, Diederichs K, Joosten RP, Keller P, Moriarty NW, Sobolev OV, Velankar S, Vonrhein C, Waterman DG, Kurisu G, Berman HM, Burley SK, Peisach E.

J Mol Biol, 2022

doi:10.1016/j.jmb.2022.167599.

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.

Varadi M, Anyango S, Deshpande M, Nair S, Natassia C, Yordanova G, Yuan D, Stroe O, Wood G, Laydon A, Žídek A, Green T, Tunyasuvunakool K, Petersen S, Jumper J, Clancy E, Green R, Vora A, Lutfi M, Figurnov M, Cowie A, Hobbs N, Kohli P, Kleywegt G, Birney E, Hassabis D, Velankar S.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab1061.

PDBe-KB: collaboratively defining the biological context of structural data.

PDBe-KB consortium.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab988.

How to interpret AlphaFold structures

Bateman A, Velankar S, Tunyasuvakool K, Ovchinnikov S, Beltrao P, Mészáros B.

2021

doi:10.6019/tol.alphafold-w.2021.00001.1.

Characterizing and explaining impact of disease-associated mutations in proteins without known structures or structural homologues

Sen N, Anishchenko I, Bordin N, Sillitoe I, Velankar S, Baker D, Orengo C.

2021

doi:10.1101/2021.11.17.468998.

A structural biology community assessment of AlphaFold 2 applications

Akdel M, Pires DEV, Porta Pardo E, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Ruiz Serra V, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Lindorff-Larsen K, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P.

2021

doi:10.1101/2021.09.26.461876.

New restraints and validation approaches for nucleic acid structures in PDB-REDO.

de Vries I, Kwakman T, Lu XJ, Hekkelman ML, Deshpande M, Velankar S, Perrakis A, Joosten RP.

Acta Crystallogr D Struct Biol, 2021

doi:10.1107/s2059798321007610.

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Giełdoń A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, Zięba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkūnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Xu X, Zhang S, Zou X, Wodak SJ.

Proteins, 2021

doi:10.1002/prot.26222.

PDBeCIF: an open-source mmCIF/CIF parsing and processing package.

van Ginkel G, Pravda L, Dana JM, Varadi M, Keller P, Anyango S, Velankar S.

BMC Bioinformatics, 2021

doi:10.1186/s12859-021-04271-9.

Highly accurate protein structure prediction for the human proteome.

Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, Bridgland A, Cowie A, Meyer C, Laydon A, Velankar S, Kleywegt GJ, Bateman A, Evans R, Pritzel A, Figurnov M, Ronneberger O, Bates R, Kohl SAA, Potapenko A, Ballard AJ, Romera-Paredes B, Nikolov S, Jain R, Clancy E, Reiman D, Petersen S, Senior AW, Kavukcuoglu K, Birney E, Kohli P, Jumper J, Hassabis D.

Nature, 2021

doi:10.1038/s41586-021-03828-1.

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data.

Nair S, Váradi M, Nadzirin N, Pravda L, Anyango S, Mir S, Berrisford J, Armstrong D, Gutmanas A, Velankar S.

Bioinformatics, 2021

doi:10.1093/bioinformatics/btab424.

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.

Shao C, Feng Z, Westbrook JD, Peisach E, Berrisford J, Ikegawa Y, Kurisu G, Velankar S, Burley SK, Young JY.

Glycobiology, 2021

doi:10.1093/glycob/cwab039.

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.

Sehnal D, Bittrich S, Deshpande M, Svobodová R, Berka K, Bazgier V, Velankar S, Burley SK, Koča J, Rose AS.

Nucleic Acids Res, 2021

doi:10.1093/nar/gkab314.

The Protein Data Bank Archive.

Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL.

Methods Mol Biol, 2021

doi:10.1007/978-1-0716-1406-8_1.

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.

Feng Z, Westbrook JD, Sala R, Smart OS, Bricogne G, Matsubara M, Yamada I, Tsuchiya S, Aoki-Kinoshita KF, Hoch JC, Kurisu G, Velankar S, Burley SK, Young JY.

Structure, 2021

doi:10.1016/j.str.2021.02.004.

High-performance macromolecular data delivery and visualization for the web. Corrigendum.

Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J.

Acta Crystallogr D Struct Biol, 2021

doi:10.1107/s205979832001606x.

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.

Waman VP, Sen N, Varadi M, Daina A, Wodak SJ, Zoete V, Velankar S, Orengo C.

Brief Bioinform, 2021

doi:10.1093/bib/bbaa362.

High-performance macromolecular data delivery and visualization for the web.

Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J.

Acta Crystallogr D Struct Biol, 2020

doi:10.1107/s2059798320014515.

BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.

Sehnal D, Bittrich S, Velankar S, Koča J, Svobodová R, Burley SK, Rose AS.

PLoS Comput Biol, 2020

doi:10.1371/journal.pcbi.1008247.

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AM, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B.

2020

doi:10.12688/f1000research.20559.1.

Modeling protein interactions and complexes in CAPRI: Seventh CAPRI evaluation meeting, April 3-5 EMBL-EBI, Hinxton, UK.

Wodak SJ, Velankar S, Sternberg MJE.

Proteins, 2020

doi:10.1002/prot.25883.

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, 2020

doi:10.1093/bioinformatics/btz959.

Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition.

Lensink MF, Nadzirin N, Velankar S, Wodak SJ.

Proteins, 2020

doi:10.1002/prot.25870.

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 Res, 2020

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 Res, 2020

doi:10.1093/nar/gkz990.

PDBe-KB: a community-driven resource for structural and functional annotations.

PDBe-KB consortium.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz853.

West-Life: A Virtual Research Environment for structural biology.

Morris C, Andreetto P, Banci L, Bonvin AMJJ, Chojnowski G, Cano LD, Carazo JM, Conesa P, Daenke S, Damaskos G, Giachetti A, Haley NEC, Hekkelman ML, Heuser P, Joosten RP, Kouřil D, Křenek A, Kulhánek T, Lamzin VS, Nadzirin N, Perrakis A, Rosato A, Sanderson F, Segura J, Schaarschmidt J, Sobolev E, Traldi S, Trellet ME, Velankar S, Verlato M, Winn M.

J Struct Biol X, 2019

doi:10.1016/j.yjsbx.2019.100006.

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, 2019

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 Crystallogr F Struct Biol Commun, 2019

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, 2019

doi:10.1002/prot.25838.

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 Crystallogr D Struct Biol, 2019

doi:10.1107/s2059798319004522.

Finding enzyme cofactors in Protein Data Bank.

Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S.

Bioinformatics, 2019

doi:10.1093/bioinformatics/btz115.

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 Res, 2019

doi:10.1093/nar/gky1114.

Protein Data Bank: the single global archive for 3D macromolecular structure data.

wwPDB consortium.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky949.

Structural biology data archiving - where we are and what lies ahead.

Kleywegt GJ, Velankar S, Patwardhan A.

FEBS Lett, 2018

doi:10.1002/1873-3468.13086.

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 (Oxford), 2018

doi:10.1093/database/bay002.

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 Crystallogr D Struct Biol, 2018

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 Crystallogr D Struct Biol, 2018

doi:10.1107/s2059798318002541.

The challenge of modeling protein assemblies: the CASP12-CAPRI experiment.

Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ.

Proteins, 2018

doi:10.1002/prot.25419.

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 Res, 2018

doi:10.1093/nar/gkx1070.

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.

Nat Methods, 2017

doi:10.1038/nmeth.4499.

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, 2017

doi:10.1016/j.str.2017.10.009.

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, 2017

doi:10.1016/j.str.2017.08.001.

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.

Methods Mol Biol, 2017

doi:10.1007/978-1-4939-7000-1_26.

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, 2017

doi:10.1016/j.str.2017.01.004.

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition.

Lensink MF, Velankar S, Wodak SJ.

Proteins, 2017

doi:10.1002/prot.25215.

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.

Sci Adv, 2016

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.

Curr Opin Struct Biol, 2016

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, 2016

doi:10.1002/prot.25007.

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.

F1000Res, 2016

doi:10.12688/f1000research.7911.1.

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, 2016

doi:10.1016/j.str.2016.02.017.

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 Res, 2016

doi:10.1093/nar/gkv1047.

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, 2015

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.

Nat Struct Mol Biol, 2015

doi:10.1038/nsmb.3041.

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, 2015

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 Res, 2015

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 Res, 2015

doi:10.1093/nar/gku975.

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 Res, 2014

doi:10.1093/nar/gkt1180.

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, 2013

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, 2013

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, 2013

doi:10.1093/bioinformatics/btt100.

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, 2013

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 Res, 2013

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 Res, 2013

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 Res, 2013

doi:10.1093/nar/gks1112.

Implementing an X-ray validation pipeline for the Protein Data Bank.

Gore S, Velankar S, Kleywegt GJ.

Acta Crystallogr D Biol Crystallogr, 2012

doi:10.1107/s0907444911050359.

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, 2012

doi:10.1107/s1744309112002618.

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, 2012

doi:10.1093/nar/gkr998.

PDBe: quick tour

Velankar S, Battle G.

2011

doi:10.6019/tol.pdbe-qt.2011.00001.1.

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, 2011

doi:10.1038/nmeth.1637.

The Protein Data Bank in Europe (PDBe): bringing structure to biology.

Velankar S, Kleywegt GJ.

Acta Crystallogr D Biol Crystallogr, 2011

doi:10.1107/s090744491004117x.

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, 2011

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 Res, 2011

doi:10.1093/nar/gkq880.

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, 2010

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, 2010

doi:10.1093/nar/gkp916.

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, 2008

doi:10.1093/nar/gkm937.

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 Res, 2006

doi:10.1093/nar/gkj163.

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, 2005

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, 2005

doi:10.1093/nar/gki058.

Unconventional interactions between water and heterocyclic nitrogens in protein structures.

Stollar EJ, Gelpí JL, Velankar S, Golovin A, Orozco M, Luisi BF.

Proteins, 2004

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 Res, 2004

doi:10.1093/nar/gkh078.

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, 2003

doi:10.1093/nar/gkg065.

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, 1999

doi:10.1006/jmbi.1999.2873.

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, 1999

doi:10.1110/ps.8.4.930.

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, 1999

doi:10.1016/s0092-8674(00)80716-3.

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, 1997

doi:10.1016/s0969-2126(97)00230-x.