J
Jose M. Dana
Researcher at European Bioinformatics Institute
Publications - 12
Citations - 1803
Jose M. Dana is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: UniProt & Protein Data Bank. The author has an hindex of 11, co-authored 12 publications receiving 1314 citations. Previous affiliations of Jose M. Dana include Wellcome Trust.
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Journal ArticleDOI
Protein Data Bank: the single global archive for 3D macromolecular structure data
Stephen K. Burley,Helen M. Berman,Charmi Bhikadiya,Chunxiao Bi,Li Chen,Luigi Di Costanzo,Cole Christie,Jose M. Duarte,Shuchismita Dutta,Zukang Feng,Sutapa Ghosh,David S. Goodsell,Rachel Kramer Green,Vladimir Guranovic,Dmytro Guzenko,Brian P. Hudson,Yu-He Liang,Robert Lowe,Ezra Peisach,Irina Periskova,Chris Randle,Alexander S. Rose,Monica Sekharan,Chenghua Shao,Yi-Ping Tao,Yana Valasatava,Maria Voigt,John D. Westbrook,Jasmine Young,Christine Zardecki,Marina A. Zhuravleva,Genji Kurisu,Haruki Nakamura,Yumiko Kengaku,Hasumi Cho,Junko Sato,Ju Yaen Kim,Yasuyo Ikegawa,Atsushi Nakagawa,Reiko Yamashita,Takahiro Kudou,Gert-Jan Bekker,Hirofumi Suzuki,Takeshi Iwata,Masashi Yokochi,Naohiro Kobayashi,Toshimichi Fujiwara,Sameer Velankar,Gerard J. Kleywegt,Stephen Anyango,David R. Armstrong,John M. Berrisford,Matthew J. Conroy,Jose M. Dana,Mandar Deshpande,Paul Gane,Romana Gáborová,Deepti Gupta,Aleksandras Gutmanas,Jaroslav Koča,Lora Mak,Saqib Mir,Abhik Mukhopadhyay,Nurul Nadzirin,Sreenath Nair,Ardan Patwardhan,Typhaine Paysan-Lafosse,Lukáš Pravda,Osman Salih,David Sehnal,Mihaly Varadi,Radka Svobodová Vařeková,John L. Markley,Jeffrey C. Hoch,Pedro Romero,Kumaran Baskaran,Dimitri Maziuk,Eldon L. Ulrich,Jonathan R. Wedell,Hongyang Yao,Miron Livny,Yannis Ioannidis +81 more
TL;DR: Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific ww PDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.
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PSICQUIC and PSISCORE: accessing and scoring molecular interactions
Bruno Aranda,Hagen Blankenburg,Samuel Kerrien,Fiona S. L. Brinkman,Arnaud Ceol,Emilie Chautard,Jose M. Dana,Javier De Las Rivas,Marine Dumousseau,Eugenia Galeota,Anna Gaulton,Johannes B. Goll,Robert E. W. Hancock,Ruth Isserlin,Rafael C. Jimenez,Jules Kerssemakers,Jyoti Khadake,David J. Lynn,Magali Michaut,Gavin O'Kelly,Keiichiro Ono,Sandra Orchard,Carlos Prieto,Sabry Razick,Olga Rigina,Lukasz Salwinski,Milan Simonovic,Sameer Velankar,Andrew G. Winter,Guanming Wu,Gary D. Bader,Gianni Cesareni,Ian Donaldson,David Eisenberg,Gerard J. Kleywegt,John P. Overington,Sylvie Ricard-Blum,Mike Tyers,Mario Albrecht,Henning Hermjakob +39 more
TL;DR: To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood.
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SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
Sameer Velankar,Jose M. Dana,Julius O.B. Jacobsen,Glen van Ginkel,Paul Gane,Jie Luo,Thomas J. Oldfield,Claire O'Donovan,Maria Jesus Martin,Gerard J. Kleywegt +9 more
TL;DR: The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database.
Journal ArticleDOI
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Jose M. Dana,Aleksandras Gutmanas,Nidhi Tyagi,Guoying Qi,Claire O'Donovan,Maria Jesus Martin,Sameer Velankar +6 more
TL;DR: The recently released implementation of SIFTS includes support for multiple cross-references for proteins in the PDB, allowing mappings to UniProtKB isoforms and UniRef90 cluster members, and makes structure data in thePDB readily available to over 1.8 million UniProt KB accessions.
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.