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Nurul Nadzirin
Researcher at European Bioinformatics Institute
Publications - 8
Citations - 508
Nurul Nadzirin is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: The Internet & Macromolecular docking. The author has an hindex of 5, co-authored 8 publications receiving 329 citations.
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Journal ArticleDOI
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB
Sameer Velankar,Glen van Ginkel,Younes Alhroub,Gary M. Battle,John M. Berrisford,Matthew J. Conroy,Jose M. Dana,Swanand Gore,Aleksandras Gutmanas,Pauline Haslam,Pieter M. S. Hendrickx,Ingvar Lagerstedt,Saqib Mir,Manuel A. Fernandez Montecelo,Abhik Mukhopadhyay,Thomas J. Oldfield,Ardan Patwardhan,Eduardo Sanz-García,Sanchayita Sen,Robert A. Slowley,Michael E. Wainwright,Mandar Deshpande,Andrii Iudin,Gaurav Sahni,José Salavert Torres,Miriam Hirshberg,Lora Mak,Nurul Nadzirin,David R. Armstrong,Alice R. Clark,Oliver S. Smart,Paul K. Korir,Gerard J. Kleywegt +32 more
TL;DR: A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource.
Journal ArticleDOI
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Marc F. Lensink,Guillaume Brysbaert,Nurul Nadzirin,Sameer Velankar,Raphael A. G. Chaleil,Tereza Gerguri,Paul A. Bates,Elodie Laine,Alessandra Carbone,Alessandra Carbone,Sergei Grudinin,Ren Kong,Ranran Liu,Xu Ximing,Hang Shi,Shan Chang,Miriam Eisenstein,Agnieszka S. Karczyńska,Cezary Czaplewski,Emilia A. Lubecka,Agnieszka G. Lipska,Paweł Krupa,Magdalena A. Mozolewska,Łukasz Golon,Sergey A. Samsonov,Adam Liwo,Adam Liwo,Silvia Crivelli,Guillaume Pagès,Mikhail Karasikov,Maria Kadukova,Maria Kadukova,Yumeng Yan,Sheng-You Huang,Mireia Rosell,Mireia Rosell,Luis A. Rodríguez-Lumbreras,Luis A. Rodríguez-Lumbreras,Miguel Romero-Durana,Lucía Díaz-Bueno,Juan Fernández-Recio,Juan Fernández-Recio,Charles Christoffer,Genki Terashi,Woong-Hee Shin,Tunde Aderinwale,Sai Raghavendra Maddhuri Venkata Subraman,Daisuke Kihara,Dima Kozakov,Sandor Vajda,Kathyn Porter,Dzmitry Padhorny,Israel Desta,Dmitri Beglov,Mikhail Ignatov,Sergey Kotelnikov,Sergey Kotelnikov,Iain H. Moal,David W. Ritchie,Isaure Chauvot de Beauchêne,Bernard Maigret,Marie-Dominique Devignes,Maria Elisa Ruiz Echartea,Didier Barradas-Bautista,Zhen Cao,Luigi Cavallo,Romina Oliva,Yue Cao,Yang Shen,Minkyung Baek,Taeyong Park,Hyeonuk Woo,Chaok Seok,M. Braitbard,Lirane Bitton,Dina Scheidman-Duhovny,Justas Dapkūnas,Kliment Olechnovič,Česlovas Venclovas,Petras J. Kundrotas,Saveliy Belkin,Devlina Chakravarty,Varsha D. Badal,Ilya A. Vakser,Thom Vreven,Sweta Vangaveti,Tyler M. Borrman,Zhiping Weng,Johnathan D. Guest,Ragul Gowthaman,Brian G. Pierce,Xianjin Xu,Rui Duan,Liming Qiu,Jie Hou,Benjamin Ryan Merideth,Zhiwei Ma,Jianlin Cheng,Xiaoqin Zou,Panos Koukos,Jorge Roel-Touris,Francesco Ambrosetti,Cunliang Geng,Jörg Schaarschmidt,Mikael Trellet,Adrien S. J. Melquiond,Li C. Xue,Brian Jiménez-García,Charlotte W. van Noort,Rodrigo V. Honorato,Alexandre M. J. J. Bonvin,Shoshana J. Wodak +111 more
TL;DR: CAPRI Round 46 indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.
Journal ArticleDOI
PDBe: improved findability of macromolecular structure data in the PDB.
David R. Armstrong,John M. Berrisford,Matthew J. Conroy,Aleksandras Gutmanas,Stephen Anyango,Preeti Choudhary,Alice R. Clark,Jose M. Dana,Mandar Deshpande,Roisin Dunlop,Paul Gane,Romana Gáborová,Deepti Gupta,Pauline Haslam,Jaroslav Koča,Lora Mak,Saqib Mir,Abhik Mukhopadhyay,Nurul Nadzirin,Sreenath Nair,Typhaine Paysan-Lafosse,Lukáš Pravda,David Sehnal,Osman Salih,Oliver S. Smart,James Tolchard,Mihaly Varadi,Radka SvobodováVařeková,Hossam Zaki,Gerard J. Kleywegt,Sameer Velankar +30 more
TL;DR: The enrichment of data at PDBe is detailed, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors and an advanced search facility with ∼100 data categories and sequence searches.
Journal ArticleDOI
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.
Saqib Mir,Younes Alhroub,Stephen Anyango,David R. Armstrong,John M. Berrisford,Alice R. Clark,Matthew J. Conroy,Jose M. Dana,Mandar Deshpande,Deepti Gupta,Aleksandras Gutmanas,Pauline Haslam,Lora Mak,Abhik Mukhopadhyay,Nurul Nadzirin,Typhaine Paysan-Lafosse,David Sehnal,Sanchayita Sen,Oliver S. Smart,Mihaly Varadi,Gerard J. Kleywegt,Sameer Velankar +21 more
TL;DR: A library of Web components which can be easily reused to port data and functionality available at PDBe to other services are introduced, and updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API are introduced.
Journal ArticleDOI
Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition
TL;DR: Analysis indicates that progress in predicting increasingly challenging and diverse types of targets is due to closer integration of template‐based modeling techniques with docking, scoring, and model refinement procedures, and to significant incremental improvements in the underlying methodologies.