Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Autor: Marcin Wojdyr, Paul D. Adams, David G. Brown, Zukang Feng, Yasuyo Ikegawa, Lora Mak, Minyu Chen, Billy K. Poon, John D. Westbrook, Ezra Peisach, Jasmine Young, Helen M. Berman, Masashi Yokochi, Nigel W. Moriarty, Yu-He Liang, Stephen K. Burley, John L. Markley, Garib N. Murshudov, John M. Berrisford, Eldon L. Ulrich, Sameer Velankar, Yumiko Kengaku, Aleksandras Gutmanas, Dorothee Liebschner, C. Flensburg, Pavel V. Afonine, Kumaran Baskaran, Clemens Vonrhein, Jeffrey C. Hoch, Eugene Krissinel, Irina Persikova, Genji Kurisu, Oleg V. Sobolev, Martin E.M. Noble, Gérard Bricogne

Publikováno v: Acta crystallographica. Section D, Structural biology, vol 75, iss Pt 4

This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::88e593a136cedb0a65b4e5c2e32df2a6
https://doi.org/10.1107/s2059798319004522

PyBMRB: Data visualization tool for BioMagResBank

Autor: Jonathan R. Wedell, John L. Markley, Jeffery C. Hoch, Kumaran Baskaran, Eldon L. Ulrich

Publikováno v: Proceedings of the Python in Science Conference.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::ea4c127f14b50f844f73826fd198c6f6
https://doi.org/10.25080/majora-1b6fd038-00a

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

Autor: Masashi Yokochi, Ju Yaen Kim, Chenghua Shao, John M. Berrisford, Hongyang Yao, Miron Livny, Stephen Anyango, Abhik Mukhopadhyay, Romana Gáborová, Yi-Ping Tao, Monica Sekharan, Aleksandras Gutmanas, Jose M. Dana, Mandar Deshpande, Charmi Bhikadiya, Yannis Ioannidis, Pedro Romero, Jonathan R. Wedell, Eldon L. Ulrich, Gert-Jan Bekker, Chris Randle, Chunxiao Bi, Jeffrey C. Hoch, Nurul Nadzirin, Jaroslav Koča, Yumiko Kengaku, Jasmine Young, Cole Christie, John D. Westbrook, Naohiro Kobayashi, Alexander S. Rose, Sameer Velankar, David Sehnal, Lukáš Pravda, David R. Armstrong, Hasumi Cho, Genji Kurisu, Lora Mak, John L. Markley, Saqib Mir, Sutapa Ghosh, Ardan Patwardhan, Zukang Feng, Stephen K. Burley, Robert Lowe, David S. Goodsell, Hirofumi Suzuki, Maria Voigt, Paul Gane, Jose M. Duarte, Osman Salih, Irina Periskova, Matthew J. Conroy, Toshimichi Fujiwara, Yasuyo Ikegawa, Takahiro Kudou, Dimitri Maziuk, Typhaine Paysan-Lafosse, Brian P. Hudson, Christine Zardecki, Sreenath Nair, Gerard J. Kleywegt, Marina A. Zhuravleva, Shuchismita Dutta, Dmytro Guzenko, Kumaran Baskaran, Rachel Kramer Green, Ezra Peisach, Li Chen, Reiko Yamashita, Vladimir Guranovic, Yu-He Liang, Takeshi Iwata, Atsushi Nakagawa, Haruki Nakamura, Junko Sato, Radka Svobodová Vařeková, Helen M. Berman, Deepti Gupta, Luigi Di Costanzo, Mihaly Varadi, Yana Valasatava

Publikováno v: Nucleic Acids Research

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::270875b3782759eb0deca83927e6993c
https://doi.org/10.1093/nar/gky949

Validation of Structures in the Protein Data Bank

Autor: Zukang Feng, John D. Westbrook, Monica Sekharan, Yasuyo Ikegawa, Haruki Nakamura, Stephen K. Burley, Pieter M. S. Hendrickx, Chenghua Shao, Kumaran Baskaran, Aleksandras Gutmanas, Sameer Velankar, Eduardo Sanz Garcia, Ezra Peisach, Ardan Patwardhan, Thomas J. Oldfield, Catherine L. Lawson, John L. Markley, Helen M. Berman, Oliver S. Smart, John M. Berrisford, Swanand Gore, Eldon L. Ulrich, Abhik Mukhopadhyay, Gaurav Sahni, Jasmine Young, Sanchayita Sen, Gerard J. Kleywegt, Martha Quesada, Huanwang Yang, Naohiro Kobayashi, Reiko Yamashita, Brian P. Hudson, Steve Mading, Lora Mak

Publikováno v: Structure(London, England:1993)
Structure
PubMed Central

Summary The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These repo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e5787d7df0b18c43851a67b2f8e9f3be
http://europepmc.org/articles/PMC5718880

Probabilistic validation of protein NMR chemical shift assignments

Autor: Marco Tonelli, John L. Markley, Woonghee Lee, Eldon L. Ulrich, Gabriel Cornilescu, Hesam Dashti, William M. Westler

Publikováno v: Europe PubMed Central
Journal of Biomolecular NMR
PubMed Central
UnpayWall
ORCID
Microsoft Academic Graph

Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::60d080739b89092610fe44e623860528
https://doi.org/10.1007/s10858-015-0007-8