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Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

A. R. Kinjo, H. Suzuki, R. Yamashita, Y. Ikegawa, T. Kudou, R. Igarashi, Y. Kengaku, H. Cho, D. M. Standley, A. Nakagawa, H. Nakamura
<span title="2011-10-05">2011</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 Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized  ...  FUNDING Funding for open access charge: National Bioscience Database Center, the Japan Science and Technology Agency. Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr811">doi:10.1093/nar/gkr811</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21976737">pmid:21976737</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245181/">pmcid:PMC3245181</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rgdsfxvkfvhgnnpag3funh52pu">fatcat:rgdsfxvkfvhgnnpag3funh52pu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219170607/http://pdfs.semanticscholar.org/18c2/7776acbd7f5646e32c512eddc2c3107b3a00.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/18/c2/18c27776acbd7f5646e32c512eddc2c3107b3a00.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr811"> <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/PMC3245181" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PDBj-BMRB : Publishing NMR Spectroscopy Derived Data of BioMagResBank in Structured Data Formats, XML and RDF(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

Masashi Yokochi
<span title="">2013</span> <i title="Biophysical Society of Japan"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fci57bxfsffvzllbssocnfsr3e" style="color: black;">Seibutsu Butsuri</a> </i> &nbsp;
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB, http://wwpdbj.org/) and accepts and processes the deposited data of experimentally determined  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized  ...  Language (XML) and a Resource Description Framework (RDF).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2142/biophys.53.s286_3">doi:10.2142/biophys.53.s286_3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gs5cgv4akrfxriqsubclnvz6hy">fatcat:gs5cgv4akrfxriqsubclnvz6hy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181101093349/https://www.jstage.jst.go.jp/article/biophys/53/supplement1-2/53_KJ00009361075/_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/f8/bd/f8bdb8af57a6f787374239d377aba81ebe1b3feb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2142/biophys.53.s286_3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

The new PDBj web Interface : Customizable, Modern and User-friendly(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

Gert-Jan Bekker
<span title="">2013</span> <i title="Biophysical Society of Japan"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fci57bxfsffvzllbssocnfsr3e" style="color: black;">Seibutsu Butsuri</a> </i> &nbsp;
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB, http://wwpdbj.org/) and accepts and processes the deposited data of experimentally determined  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized  ...  Language (XML) and a Resource Description Framework (RDF).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2142/biophys.53.s286_2">doi:10.2142/biophys.53.s286_2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jwa4gpvwu5bwxbkuytbjfsptxm">fatcat:jwa4gpvwu5bwxbkuytbjfsptxm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724165117/https://www.jstage.jst.go.jp/article/biophys/53/supplement1-2/53_KJ00009361074/_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/b7/ab/b7ab2b61f121952d03aa1f3795d71f4452966e9c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2142/biophys.53.s286_2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Activities of PDBj and wwPDB : A new PDB format, Data Deposition, Validation, and Data Integration(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

Haruki Nakamura
<span title="">2013</span> <i title="Biophysical Society of Japan"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fci57bxfsffvzllbssocnfsr3e" style="color: black;">Seibutsu Butsuri</a> </i> &nbsp;
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB, http://wwpdbj.org/) and accepts and processes the deposited data of experimentally determined  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized  ...  Language (XML) and a Resource Description Framework (RDF).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2142/biophys.53.s286_1">doi:10.2142/biophys.53.s286_1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5bl4c43nubeajjjpewlmpuavve">fatcat:5bl4c43nubeajjjpewlmpuavve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181101234010/https://www.jstage.jst.go.jp/article/biophys/53/supplement1-2/53_KJ00009361073/_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/89/34/8934bf36775e2d92ed732a96eb8cc3135f8877ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2142/biophys.53.s286_1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata (+4 others)
<span title="2017-09-18">2017</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures.  ...  In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated  ...  Introduction The Protein Data Bank Japan (PDBj, https://pdbj. org/) 1,2 accepts and annotates biological macromolecular structure data in collaboration with the other worldwide Protein Data Bank (wwPDB  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.3273">doi:10.1002/pro.3273</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28815765">pmid:28815765</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5734392/">pmcid:PMC5734392</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7ttn55ucxvcjfjkmivznvmet34">fatcat:7ttn55ucxvcjfjkmivznvmet34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211004359/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5734392&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/65/1c/651ccaafc49f61b36c0e77358966897fa7babf49.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.3273"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734392" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
<span title="2016-10-26">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 Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (ww-PDB), accepts and processes the deposited data of experimentally determined macromolecular structures  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins.  ...  ACKNOWLEDGEMENTS The authors thank the PDBj annotators, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Junko Sato for their constant effort that makes the wwPDB possible at all, and Reiko Yamashita and Takahiro  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw962">doi:10.1093/nar/gkw962</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27789697">pmid:27789697</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5210648/">pmcid:PMC5210648</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pan6qdrpe5bknfgkot6blgnp6u">fatcat:pan6qdrpe5bknfgkot6blgnp6u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308035501/http://pdfs.semanticscholar.org/ec1e/16eecddb163ea1a8b5e1c91b7110bfce5567.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/ec/1e/ec1e16eecddb163ea1a8b5e1c91b7110bfce5567.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw962"> <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/PMC5210648" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PDBML: the representation of archival macromolecular structure data in XML

J. Westbrook, N. Ito, H. Nakamura, K. Henrick, H. M. Berman
<span title="2004-10-27">2004</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) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML.  ...  Availability: The current software translated XML schema file is located at http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd, and on the PDB mmCIF resource page at  ...  The Protein Data Bank (PDB) (Bernstein et al., 1977; Berman et al., 2000) is the single worldwide repository for macromolecular structure data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti082">doi:10.1093/bioinformatics/bti082</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15509603">pmid:15509603</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2qvqbtgyqjbrdkkam3zt5lrau4">fatcat:2qvqbtgyqjbrdkkam3zt5lrau4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20090219074755/http://bioinformatics.oxfordjournals.org:80/cgi/reprint/21/7/988.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/39/52/395272ac572a587b3ae53a187be81777ec04dfe2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti082"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

How Community Has Shaped the Protein Data Bank

Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
Over the last 40 years, the Protein Data Bank (PDB) has grown from a small data repository promoted by the structural biology community to a critical international resource used around the world in a broad  ...  Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules.  ...  ACKNOWLEDGMENTS The wwPDB thanks staff past and present and all members of the PDB community.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2013.07.010">doi:10.1016/j.str.2013.07.010</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24010707">pmid:24010707</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4435976/">pmcid:PMC4435976</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ifkxbpcv35eoln3w34jgxmymfq">fatcat:ifkxbpcv35eoln3w34jgxmymfq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210062129/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4435976&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/87/be/87bedb4443b6f7b18bffe0895ac73c33752c011a.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.2013.07.010"> <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/PMC4435976" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank

John D. Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young
<span title="2014-12-02">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank entries.  ...  Availability and Implementation: The CCD is updated regularly in conjunction with the scheduled weekly release of new PDB structure data.  ...  We thank Helen Berman (RCSB PDB) for her leadership, long-standing support for developing data standards, and assistance in the preparation of this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu789">doi:10.1093/bioinformatics/btu789</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25540181">pmid:25540181</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4393513/">pmcid:PMC4393513</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k6buqviz3rcuhclavmpmzn233u">fatcat:k6buqviz3rcuhclavmpmzn233u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160108235043/http://bioinformatics.oxfordjournals.org:80/content/early/2014/12/02/bioinformatics.btu789.full.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/a8/71/a871795b9368bc228c964b8401b9d12e4b5b5510.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu789"> <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/PMC4393513" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Crystallography and Databases

Ian Bruno, Saulius Gražulis, John R Helliwell, Soorya N Kabekkodu, Brian McMahon, John Westbrook
<span title="2017-08-07">2017</span> <i title="Ubiquity Press, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6c6hoxo2t5fhvmt3alezyxsomy" style="color: black;">Data Science Journal</a> </i> &nbsp;
Crystallographic databases have existed as electronic resources for over 50 years, and have provided comprehensive archives of crystal structures of inorganic, organic, metal-organic and biological macromolecular  ...  compounds of immense value to a wide range of structural sciences.  ...  PDBj by JST-NBDC; and BMRB by the National Institute of General Medical Sciences (GM109046).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5334/dsj-2017-038">doi:10.5334/dsj-2017-038</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d7adzhjqxvf4zfcfzgaen2qf3e">fatcat:d7adzhjqxvf4zfcfzgaen2qf3e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720075817/https://datascience.codata.org/jms/article/download/dsj-2017-038/703" 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/10.5334/dsj-2017-038"> <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: 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;
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania  ...  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/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>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308003629/http://pdfs.semanticscholar.org/e963/84772807f391a7a62001631b3ec8730491e8.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/e9/63/e96384772807f391a7a62001631b3ec8730491e8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1004"> <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/PMC6324064" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PDBe: Protein Data Bank in Europe

S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman (+13 others)
<span title="2009-10-25">2009</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;
of bio-macromolecular structure data, the Protein Data Bank (PDB).  ...  The Protein Data Bank in Europe (PDBe) (http://www .ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive  ...  ACKNOWLEDGEMENTS We wish to thank all collaborators and partners in the EBI, EMBL, wwPDB and other collaborative efforts, as  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp916">doi:10.1093/nar/gkp916</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19858099">pmid:19858099</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2808887/">pmcid:PMC2808887</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/amgz3equ6jgenhym77vbghy47e">fatcat:amgz3equ6jgenhym77vbghy47e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227162157/http://pdfs.semanticscholar.org/92cc/9d94bcb514b9330fcc0897a56d254b29f3f7.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/92/cc/92cc9d94bcb514b9330fcc0897a56d254b29f3f7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp916"> <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/PMC2808887" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The data universe of structural biology

Helen M. Berman, Brinda Vallat, Catherine L. Lawson
<span title="2020-05-28">2020</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4rhfyrx7xvh4bmdqhfismcwocu" style="color: black;">IUCrJ</a> </i> &nbsp;
The Protein Data Bank (PDB) has grown from a small data resource for crystallographers to a worldwide resource serving structural biology.  ...  This network will expand the capabilities of structural biology and enable the determination and archiving of increasingly complex structures.  ...  Acknowledgements We would like to thank the members of the extended PDB family for the many years of collaboration and support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s205225252000562x">doi:10.1107/s205225252000562x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32695409">pmid:32695409</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7340255/">pmcid:PMC7340255</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mnh7usf2zfg3rljrw77gzy4k4a">fatcat:mnh7usf2zfg3rljrw77gzy4k4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200905102806/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7340255&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/38/38/3838d47386112c9385598983e51bdd5b8631f260.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s205225252000562x"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7340255" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

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>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228175031/http://pdfs.semanticscholar.org/963a/f1da956625e944509fd065cbcd6aea4f250a.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/96/3a/963af1da956625e944509fd065cbcd6aea4f250a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bay002"> <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/PMC5804564" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Semantic Web technologies for the big data in life sciences

Hongyan Wu, Atsuko Yamaguchi
<span title="">2014</span> <i title="International Research and Cooperation Association for Bio &amp; Socio-Sciences Advancement (IRCA-BSSA)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m6k4xi764fhpzp7hyda2ba3cva" style="color: black;">BioScience Trends</a> </i> &nbsp;
The paper presents a survey of big data in life sciences, big data related projects and Semantic Web technologies.  ...  To ensure that big data has a major influence in the life sciences, comprehensive data analysis across multiple data sources and even across disciplines is indispensable.  ...  Acknowledgements This work has been supported by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5582/bst.2014.01048">doi:10.5582/bst.2014.01048</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x2rlpyjel5cybarma34ji6sq3y">fatcat:x2rlpyjel5cybarma34ji6sq3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728145438/https://www.jstage.jst.go.jp/article/bst/8/4/8_2014.01048/_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/10/d4/10d44728a45b0ea5507e213b81ac49f7b83c7c6a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5582/bst.2014.01048"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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