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Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
<span title="2018-01-01">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.  ...  Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands.  ...  Acknowledgements The authors thank all the members of the worldwide Protein Data Bank (wwPDB) for their support and feedback, Kim Henrick for his direction to the PDB in Europe (PDBe) biocuration team  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bay002">doi:10.1093/database/bay002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29688351">pmid:29688351</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5804564/">pmcid:PMC5804564</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pymncvy65zghjgdhleavnz7oce">fatcat:pymncvy65zghjgdhleavnz7oce</a> </span>
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Research data management: structure factors and atomic coordinates

Stephen K. Burley
<span title="2017-12-01">2017</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rd3cuh2n4rfezc6sy4igtb5jci" style="color: black;">Acta Crystallographica Section A: Foundations and Advances</a> </i> &nbsp;
The Protein Data Bank (PDB; pdb.org) was established in 1971 as the first open-access digital data resource in biology.  ...  The mission of the wwPDB organization is to ensure that the PDB archive will continue in perpetuity as a high-quality, open-access digital data resource with no limitations on usage.  ...  Acknowledgements: The RCSB Protein Data Bank (RCSB PDB; rcsb.org) is a founding member of the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0108767317096866">doi:10.1107/s0108767317096866</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qs42vbi7fbfjxmc4xfkp2dcvg4">fatcat:qs42vbi7fbfjxmc4xfkp2dcvg4</a> </span>
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RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh (+28 others)
<span title="2018-10-24">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
in support of a 'Structural View of Biology.'  ...  and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around  ...  ACKNOWLEDGEMENTS RCSB PDB is a member of the Worldwide Protein Data Bank (wwPDB.org).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1004">doi:10.1093/nar/gky1004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30357411">pmid:30357411</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6324064/">pmcid:PMC6324064</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/clctmqo6ujaifm7s27vk3s2h7i">fatcat:clctmqo6ujaifm7s27vk3s2h7i</a> </span>
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RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

Stephen K. Burley, Helen M. Berman, Cole Christie, Jose M. Duarte, Zukang Feng, John Westbrook, Jasmine Young, Christine Zardecki
<span title="2017-11-11">2017</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org).  ...  The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International  ...  ; 3D electron microscopy; integrative/hybrid methods; data archive; macromolecular structure; biocuration; validation; metadata; FAIR principles; open access; data deposition Introduction: Protein Data  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.3331">doi:10.1002/pro.3331</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29067736">pmid:29067736</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5734314/">pmcid:PMC5734314</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7jdrdkkw6ffffeu2xpsqp3le4i">fatcat:7jdrdkkw6ffffeu2xpsqp3le4i</a> </span>
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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)
<span title="2018-10-24">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
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  ...  The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules.  ...  INTRODUCTION The Protein Data Bank (PDB, pdb.org) was established in 1971 as the first open-access, molecular data resource in biology (1) .  ... 
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OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen (+37 others)
<span title="2017-02-09">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting  ...  OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration  ...  ACKNOWLEDGEMENTS The authors thank all the members of Worldwide PDB for their support and feedback, especially Kumaran Baskaran, Toshimichi Fujiwara, Takeshi  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2017.01.004">doi:10.1016/j.str.2017.01.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28190782">pmid:28190782</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5360273/">pmcid:PMC5360273</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/okamctypwvdrxfomgjio4rsvma">fatcat:okamctypwvdrxfomgjio4rsvma</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210211101/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5360273&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a6/24/a624c96a85cd7c886b2b04e50d25c4574f791ed2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2017.01.004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5360273" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Structure of the Pandemic

Sarah Kearns
<span title="2020-08-04">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
In particular, structural biology as a field was poised to quickly respond to crises due to previous experience and expertise and because of its early adoption of open access practices.  ...  During global pandemics, the spread of information needs to be faster than the spread of the virus in order to ensure the health and safety of human populations worldwide.  ...  for interesting and constructive conversations; and Kristen Verhey and Michael Cianfrocco for their mentorship, support, and encouragement.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2020.07.007">doi:10.1016/j.str.2020.07.007</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32755569">pmid:32755569</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7402234/">pmcid:PMC7402234</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wbbxaj5djbg7vbix7hxiqfnteu">fatcat:wbbxaj5djbg7vbix7hxiqfnteu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200904192620/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7402234&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2020.07.007"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402234" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development

Stephen K. Burley
<span title="2021-03-17">2021</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mryncoafc5cxdicldzfm4vlsze" style="color: black;">Journal of Biological Chemistry</a> </i> &nbsp;
Finally, the author gratefully acknowledges contributions to the success of the PDB archive made by all members of RCSB PDB (past and present) and our Worldwide Protein Data Bank partners (Protein Data  ...  Bank in Europe, Protein Data Bank Japan, Biological Magnetic Resonance Bank, and Electron Microscopy Data Bank).  ...  Bioinformatics Protein Data Bank and coleader of the Worldwide Protein Data Bank (wwPDB) partnership (see below).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbc.2021.100559">doi:10.1016/j.jbc.2021.100559</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33744282">pmid:33744282</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7aumkkjssrbn3mmx5k4jwvenoa">fatcat:7aumkkjssrbn3mmx5k4jwvenoa</a> </span>
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RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

David S Goodsell, Stephen K Burley
<span title="2020-09-16">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3xwigx3kbzej7bhsigycvwxwiq" style="color: black;">Oncogene</a> </i> &nbsp;
The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers  ...  Protein Data Bank (PDB).  ...  RCSB PDB is jointly funded by grants to SKB from the National Science Foundation (DBI-1832184), the US Department of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41388-020-01461-2">doi:10.1038/s41388-020-01461-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32939013">pmid:32939013</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7581513/">pmcid:PMC7581513</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bhnkikcx6rbxjkqgqzmdzzthmq">fatcat:bhnkikcx6rbxjkqgqzmdzzthmq</a> </span>
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OUP accepted manuscript

<span title="">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb. org), the US data center for the global PDB archive, makes PDB data freely available to all users, from  ...  New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.'  ...  ACKNOWLEDGEMENTS RCSB PDB is a member of the Worldwide Protein Data Bank (wwPDB.org).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw1000">doi:10.1093/nar/gkw1000</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27794042">pmid:27794042</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5210513/">pmcid:PMC5210513</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7snb5xj2bjbxxklorxm5kwax6i">fatcat:7snb5xj2bjbxxklorxm5kwax6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223185819/http://pdfs.semanticscholar.org/54c3/1f9d122271ada312ee35eef9771b2a075e1f.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/54/c3/54c31f9d122271ada312ee35eef9771b2a075e1f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw1000"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210513" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

14th Annual Biocuration Conference (virtual) - Abstracts from the invited speakers talks and poster session presentations [article]

Federica Quaglia
<span title="2021-10-14">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations  ...  and Ontologies The Protein Data Bank (PDB) provides open access to >175,000 biological macromolecules that facilitate understanding of the structure and its function in biology. wwPDB collaboration and  ...  Biocuration: On the Front Line of Structural Biology", RCSB Protein Data Bank, Rutgers, The State University of New Jersey, NJ, USA. 4.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5570276">doi:10.5281/zenodo.5570276</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nlbkkzkhfvhdddqu4ypzh247iy">fatcat:nlbkkzkhfvhdddqu4ypzh247iy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211015105221/https://zenodo.org/record/5570276/files/ISB2021%20-%20abstracts%20booklet.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/63/fe/63fec20ffca3f5b0f508abf4884a9df1bfb093a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5570276"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

Chenghua Shao, Zonghong Liu, Huanwang Yang, Sijian Wang, Stephen K. Burley
<span title="">2018</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a577b42d4nfhddl7kurxnuyzem" style="color: black;">Scientific Data</a> </i> &nbsp;
structure data.  ...  Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails.  ...  Bioinformatics PDB and our Worldwide Protein Data Bank partners.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/sdata.2018.293">doi:10.1038/sdata.2018.293</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qnn7mj7weravhpmw63mtfqd3iu">fatcat:qnn7mj7weravhpmw63mtfqd3iu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200313144904/https://www.nature.com/articles/sdata2018293.pdf?error=cookies_not_supported&amp;code=10a3f407-bc59-49b7-bc34-08b45a133bae" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/72/8e727bd012ca3c9e8954a1b20ddad84cc5de71f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/sdata.2018.293"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Cole H Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M Duarte, Shuchismita Dutta, Zukang Feng (+26 others)
<span title="2020-11-19">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership  ...  , serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around  ...  ACKNOWLEDGEMENTS RCSB PDB is a member of the Worldwide Protein Data Bank (wwPDB.org).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa1038">doi:10.1093/nar/gkaa1038</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33211854">pmid:33211854</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7779003/">pmcid:PMC7779003</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dkqo54quqjgovp7y4v67b635zu">fatcat:dkqo54quqjgovp7y4v67b635zu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201209232809/https://watermark.silverchair.com/gkaa1038.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArcwggKzBgkqhkiG9w0BBwagggKkMIICoAIBADCCApkGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMys2t8AvCO7M3u1gaAgEQgIICapBNtygzZ91xv6NIXjnPAGi7DdjKdwcyN3gBiGpn5lP93hzS2gyicuP0F9ev_AzXncT1FZAgcYx_g1Ab9MFqQYc3lEUGULYB6YI_ztqd_dF2V0AlHNJaR5zsQHGutZp73t0pJWHOrW0GP9BvPJf3Ez4graBH_5RYYSVE4QOlOYZvD8q8WoStvd8TuLOXHKZJOM7711WNuKRXZst7bY0eVRRT8YOMUuCK5I8Wcjb6J8BqO23CxWhRMSZVj3BxxBflQj1ozF2ZXFb_G1xiFm1NmuuK3oQEN80eTf7VwyJyEUSntmP1MmRuBPJgOh1JlU_WwPtOUKrsFQnSOboi2TE-k4jdD_hwu0_osBgYp3gFrLUaPwAlohyhjVwBhP3KsHhgxUM1aVGzY3oa1lKGRVFwA8b5WRAA1OHGvwv8DVk_GjNyV1Bg_F9sgt4j7SK47VmRVoa5lXbuFqOdSkUhD9FHRhkF-X580hImX7BnoxC5U3gCzb04n7zF5iWmaJ8WfM0PXCLvaDTkO9FvUYxuFd7DGOvYYx5TUlhZEnNVzYdO-qypTZQ1Ct_9Zqdor8kVF8z7N8Xrv5-TlWFN4JZ0-oyUQ-F5WZi-_ew8sEtvQ7c-08yyCkDYmsZiLXA_4Sk7pf7DmqH78PjAcvnBeU-vYYvv5j5_8T60lWIdBdDG3rjAwWbFPHhTfK3bTiiIEXshgeE3d6P8ynRRq5dAWPRBZHzrIDCsx8T4UvsmkiJJnNr65KxWi6aMw7U4S26YOZ0qxH9J3D5-fmsUGTrxlojqr_perGzQ7DRKFFa2VtHbJTIOh-pAuNYmUmlwceP4gA" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/12/c2/12c21851b68653ebe0064ece45bad8895b04c7d2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa1038"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779003" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank

Andreas Prlić, Tara Kalro, Roshni Bhattacharya, Cole Christie, Stephen K. Burley, Peter W. Rose
<span title="2016-08-22">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules.  ...  This integration bridges from the human genome across protein sequence to 3D structure space.  ...  Introduction The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital resource in biology with just seven X-ray crystal structures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw547">doi:10.1093/bioinformatics/btw547</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27551105">pmid:27551105</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5167066/">pmcid:PMC5167066</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l4rrzkjyafgyhlx45uzgrexd5y">fatcat:l4rrzkjyafgyhlx45uzgrexd5y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209100832/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5167066&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/80/f1/80f14d87b662d3dea1bc4c49bff09b572c0d87f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw547"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167066" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari (+17 others)
<span title="2020-11-10">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The resource is committed to open access and reproducible science based on the FAIR data principles.  ...  Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide.  ...  that have helped us to improve the overall quality of Gramene as a community resource.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa979">doi:10.1093/nar/gkaa979</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33170273">pmid:33170273</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/atundz637bfalivwtye3vb3twe">fatcat:atundz637bfalivwtye3vb3twe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201115025812/https://watermark.silverchair.com/gkaa979.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArQwggKwBgkqhkiG9w0BBwagggKhMIICnQIBADCCApYGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMAiAJAnixDFiGpfQWAgEQgIICZ4IfDNLIzysPKzc-sqqbJAXxHJJX5MagtKGLqsaoeMqQzxk6UeH1-DC2KOUkdTc5pbabIHIUU3fJRwvpLXuesQtN87YI2L4f8QU5WUasShTaLIQfPD6QWxwFjQQMnMkXglopj6sy0bFR0pldf4AI88nfwy88X6O09WXGNhEhb7_0kyNvaizUBt9Lvc6R6tiUzoQM8A1OJbFMc2HL-_oMU-upeovMmDk8uTtatjlY9qh62jH2Bnb0spaUuN8OO3DZ0iHo1UBkRgTes5NVZLyeT4srPSvG48mJKhM2Y5imLThDFerW1u971Q8LM58caA0SXzu6Tdg69q68vZ1JaDysU7B1DtwTMtIQ6-xmxNOrFkXZcxPL9noi7gv2C7aj2MstbhDYiXba9JADqv2eJ3xhwBlZeuu393ywlrz8N2v-eGfkmo6XIR6XaaFnilsiWwA7Z0qjc3ov9PPNsISwhbO6QuyxByMokqaZWrwOCetossR7dePXMW5ASAACjkfjS3dMdeUDuKQfqFlNRdBxo42obMIfywBVoMdyO1Xx8jyi2HuIX48tHwJpmkoAP41beESZP2_WnfMI58j6vb06EigMOBF9PPI3wG4_emXiGHctoIqgm5-CWfE4UZFPavc-n-wCPjeXju8E-IIdRxOVY5rJIMm_h00uUDCAr4JquEoPkgSMa6QVQXD9L4ZnXdESgWVvUQt6_D5q6zw7AXJITyfKZU-RsGZCubitZw-RNTDjmPIiBeyxq3sXE-mlIED3ZjHSpBFf2gpId1xzUKyiWhStm14bI--u7Pao9xDPf39CKzv3_izBzLzniQ" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/11/be/11be5b4747b081e5322a9bd62a82e79a18a2cb87.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa979"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a>
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