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NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments

Eldon L. Ulrich, Kumaran Baskaran, Hesam Dashti, Yannis E. Ioannidis, Miron Livny, Pedro R. Romero, Dimitri Maziuk, Jonathan R. Wedell, Hongyang Yao, Hamid R. Eghbalnia, Jeffrey C. Hoch, John L. Markley
2018 Journal of Biomolecular NMR  
The growth of the biological nuclear magnetic resonance (NMR) field and the development of new experimental technology have mandated the revision and enlargement of the NMR-STAR ontology used to represent experiments, spectral and derived data, and supporting metadata. We present here a brief description of the NMR-STAR ontology and software tools for manipulating NMR-STAR data files, editing the files, extracting selected data, and creating data visualizations. Detailed information on these is accessible from the links provided.
doi:10.1007/s10858-018-0220-3 pmid:30580387 pmcid:PMC6441402 fatcat:zt6ecfqj7vawpop5p2o3556rda

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 (+70 others)
2018 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 international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of
more » ... proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB 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.
doi:10.1093/nar/gky949 pmid:30357364 pmcid:PMC6324056 fatcat:ca3xenxsdzgvnb7vcwi2gtomoa

PACSY, a relational database management system for protein structure and chemical shift analysis

Woonghee Lee, Wookyung Yu, Suhkmann Kim, Iksoo Chang, Weontae Lee, John L. Markley
2012 Journal of Biomolecular NMR  
We thank Dimitri Maziuk for technical support of the NMRFAM computer network.  ... 
doi:10.1007/s10858-012-9660-3 pmid:22903636 pmcid:PMC3542970 fatcat:hjkezj5m4fbkphykkcvjdmk3xy