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Design and application of a C++ macromolecular class library

W Chang, I N Shindyalov, C Pu, P E Bourne
<span title="">1994</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q33b3suvffclbkvfvrsg3ljwjm" style="color: black;">Proceedings. International Conference on Intelligent Systems for Molecular Biology</a> </i> &nbsp;
PDBlib forms the kernel of a larger software framework being developed for assiting in knowledge discovery from macromolecular structure data.  ...  PDBlib represents the structural features of proteins, DNA, RNA, and complexes thereof, at a level of detail on a par with that which can be parsed from a Protein Data Bank (PDB) entry.  ...  Acknowledgements We would like to thank Li-Chung Chang who contributed to the early PDBlib code and Eduardo Alessio who has coordinated efforts to use PDBlib in its application to PDBtool.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/7584420">pmid:7584420</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3sgjf33t6bhezimtlkoq6vfoqq">fatcat:3sgjf33t6bhezimtlkoq6vfoqq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151026214050/http://www.aaai.org/Papers/ISMB/1994/ISMB94-009.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/38/40/38403190e3d239162e0346ed7ad202eaaeae86a3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

H. Boutselakis
<span title="2003-01-01">2003</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 E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information.  ...  The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive.  ...  ACKNOWLEDGEMENTS E-MSD gratefully acknowledge the support from the Wellcome Trust (GR062025MA), the EU (TEMBLOR, NMRQUAL and IIMS), CCP4, the BBSRC, the MRC and EMBL.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg065">doi:10.1093/nar/gkg065</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12520052">pmid:12520052</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC165512/">pmcid:PMC165512</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ujv2d6orw5gr7hpqxnu647245m">fatcat:ujv2d6orw5gr7hpqxnu647245m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050329133910/http://www.ebi.ac.uk:80/msd-srv/docs/publications/pub9_03.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/17/05/1705ac7f7f7d9b184c5f4579fc220648286ccd8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg065"> <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/PMC165512" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A graphical front end for theARP/wARPsoftware in macromolecular

Gerrit G. Langer, Victor S. Lamzin
<span title="2009-08-16">2009</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/w3vqn7pfvvhztgjopipjutfgtq" style="color: black;">Acta Crystallographica Section A Foundations of Crystallography</a> </i> &nbsp;
intervention to very informed guidance of the software.  ...  This has tremendously shortened the time in which a macromolecular model could be built, from months and sometimes years to days or even a few hours.  ...  Obtaining phase information for the solution of macromolecular structures is still one of the major challenges in X-ray crystallography. 5-Amino-2,4,6-triiodoisophthalic acid (I3C) and 5-amino-2,4,6-tribromoisophthalic  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s010876730909669x">doi:10.1107/s010876730909669x</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/irv43ts5xrbovfetsyagnprnjy">fatcat:irv43ts5xrbovfetsyagnprnjy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721210214/http://journals.iucr.org/a/issues/2009/a1/00/a45330/a45330.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/53/0c/530c302c068db11ad1fe9bfa676537743cb6578d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s010876730909669x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </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>

PHENIX: building new software for automated crystallographic structure determination

Paul D. Adams, Ralf W. Grosse-Kunstleve, Li-Wei Hung, Thomas R. Ioerger, Airlie J. McCoy, Nigel W. Moriarty, Randy J. Read, James C. Sacchettini, Nicholas K. Sauter, Thomas C. Terwilliger
<span title="2002-10-21">2002</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6inoqqfovnhtledhw3uuo322xa" style="color: black;">Acta Crystallographica Section D: Biological Crystallography</a> </i> &nbsp;
This new software will provide the necessary algorithms to proceed from reduced intensity data to a re®ned molecular model and to facilitate structure solution for both the novice and expert crystallographer  ...  Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases.  ...  This work was funded by NIH/NIGMS under grant number 1P01GM063210, with initial funding to PDA from the Department of Energy under contract No. DE-AC03-76SF00098.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444902016657">doi:10.1107/s0907444902016657</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12393927">pmid:12393927</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tabjmto6zjcqbnvzktwg3xvzvq">fatcat:tabjmto6zjcqbnvzktwg3xvzvq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725023256/http://journals.iucr.org/d/issues/2002/11/00/ba5027/ba5027.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/ff/40/ff40044f597fac2f29faab86bc446fd846c9cbe9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0907444902016657"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Information-Driven Modeling of Biomolecular Complexes [article]

Charlotte W. van Noort, Rodrigo V. Honorato, Alexandre M.J.J. Bonvin
<span title="2021-03-12">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
and membrane protein complexes, and the use of evolutionary and shape information.  ...  We review here the use of experimental and bioinformatics data in protein-protein docking, describing recent software developments and highlighting applications for the modeling of antibody-antigen complexes  ...  Acknowledgments The authors acknowledge the financial support from the European Union Horizon 2020 projects BioExcel (675728, 823830).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2103.07508v1">arXiv:2103.07508v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qozkvvaazvcsfdcog3ao3hjqja">fatcat:qozkvvaazvcsfdcog3ao3hjqja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210320155019/https://arxiv.org/ftp/arxiv/papers/2103/2103.07508.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/a4/79/a4796a1acd7a1a0265c86f3c3f17f51ff0b60000.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2103.07508v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </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).  ...  maintained derived data to the existing structural data in the PDB.  ...  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>

AITom: Open-source AI platform for cryo-electron tomography data analysis [article]

Xiangrui Zeng, Min Xu
<span title="2020-10-30">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Comprehensive tutorials for each analysis module are provided to guide the user through. We welcome researchers and developers to join this collaborative open-source software development project.  ...  Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution  ...  However, major gaps exist between obtaining the raw tomogram data and decoding the macromolecular complex structural information from it.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1911.03044v2">arXiv:1911.03044v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/445x3wnfafevxm6jdiqt27khhu">fatcat:445x3wnfafevxm6jdiqt27khhu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201103001957/https://arxiv.org/pdf/1911.03044v2.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/4f/3b/4f3b02a73b7e29ecf9657356cf915f2575cad263.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1911.03044v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

An overview of the CCP4 project in protein crystallography: an example of a collaborative project

M. D. Winn
<span title="2002-12-24">2002</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/opv6emcd4vfpfltyzbw5jnivwq" style="color: black;">Journal of Synchrotron Radiation</a> </i> &nbsp;
CCP4 now distributes a large software suite and is active in developing new software.  ...  In this article, an overview is given of CCP4 activities and their administration. The emphasis is on generic features of the collaboration rather than details specific to protein crystallography.  ...  When using several programs to solve a structure, data is passed between programs using standard ®le formats.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0909049502017235">doi:10.1107/s0909049502017235</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6b2dkkk57berhdrhl2nmn77ddq">fatcat:6b2dkkk57berhdrhl2nmn77ddq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040724162712/http://www.ccp4.ac.uk:80/martyn/reprint22.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/a0/92a01a067107f2d0feaaef71c17bb786414043ef.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s0909049502017235"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Archiving and disseminating integrative structure models

Brinda Vallat, Benjamin Webb, John Westbrook, Andrej Sali, Helen M. Berman
<span title="2019-07-05">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cimmcbrwkbf4xblwfxyaslsraa" style="color: black;">Journal of Biomolecular NMR</a> </i> &nbsp;
A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force  ...  Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from  ...  We thank the wwPDB leadership and the members of the wwPDB IHM Task Force for their  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10858-019-00264-2">doi:10.1007/s10858-019-00264-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31278630">pmid:31278630</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6692293/">pmcid:PMC6692293</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zqrytg2f5razbpfkewzgwvk4ci">fatcat:zqrytg2f5razbpfkewzgwvk4ci</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200310202055/https://link.springer.com/content/pdf/10.1007%2Fs10858-019-00264-2.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/58/50/58508aabfca4fd50b530cdf3c957c8fe66f5f782.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10858-019-00264-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692293" 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 future of crystallography in drug discovery

Heping Zheng, Jing Hou, Matthew D Zimmerman, Alexander Wlodawer, Wladek Minor
<span title="2013-12-28">2013</span> <i title="Informa Healthcare"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4m2squtugrdvtgjdvfbz5jhmaq" style="color: black;">Expert Opinion on Drug Discovery</a> </i> &nbsp;
Advancements of various software packages has made use of structural information in CADD both readily accessible and automated [3] [4] [5] .  ...  Considered as a hypothesis framework, a crystal structure may be used as the basis to propose or prioritize biological assays in experimental design but should not be used to prove or rule out any hypotheses  ...  Bibliography Papers of special note have been highlighted as either of interest () or of considerable interest () to readers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1517/17460441.2014.872623">doi:10.1517/17460441.2014.872623</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24372145">pmid:24372145</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4106240/">pmcid:PMC4106240</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lc6rc2rclvbitkypuy63kbgule">fatcat:lc6rc2rclvbitkypuy63kbgule</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308052527/http://pdfs.semanticscholar.org/edb0/60de580b7ba3d83bc0a9621a60bcd2805e58.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/ed/b0/edb060de580b7ba3d83bc0a9621a60bcd2805e58.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1517/17460441.2014.872623"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4106240" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

New system for archiving integrative structures

Brinda Vallat, Benjamin Webb, Maryam Fayazi, Serban Voinea, Hongsuda Tangmunarunkit, Sai J. Ganesan, Catherine L. Lawson, John D. Westbrook, Carl Kesselman, Andrej Sali, Helen M. Berman
<span title="2021-11-29">2021</span> <i title="International Union of Crystallography (IUCr)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b3zks4nhqvgixag6suqb5wlhsu" style="color: black;">Acta Crystallographica Section D: Structural Biology</a> </i> &nbsp;
Structures of many complex biological assemblies are increasingly determined using integrative approaches, in which data from multiple experimental methods are combined.  ...  Here, the data standards and software tools that support PDB-Dev are described along with the new and updated components of the PDB-Dev data-collection, processing and archiving infrastructure.  ...  We thank all of the depositors of PDB-Dev for providing us with examples of integrative structures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2059798321010871">doi:10.1107/s2059798321010871</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34866606">pmid:34866606</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8647179/">pmcid:PMC8647179</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fadtq7rtbnfivmuse4pir4ww2u">fatcat:fadtq7rtbnfivmuse4pir4ww2u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220125124418/https://journals.iucr.org/d/issues/2021/12/00/qg5005/qg5005.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/d0/56/d056b1be7bd6d961436be34fac27b2f3b9bbce17.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1107/s2059798321010871"> <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/PMC8647179" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

E-MSD: improving data deposition and structure quality

M. Tagari
<span title="2006-01-01">2006</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 Macromolecular Structure Database (MSD)  ...  ACKNOWLEDGEMENTS E-MSD gratefully acknowledges the support of the Wellcome Trust (GR062025MA), the EU (TEMBLOR, NMRQUAL and 3D-EM NoE), CCP4, the BBSRC, the MRC and EMBL.  ...  An example of the extra data that are derived, rather than being added by the depositor, is secondary structure information: the PDB uses standard programs to generate secondary structure records, ensuring  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkj163">doi:10.1093/nar/gkj163</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16381867">pmid:16381867</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1347525/">pmcid:PMC1347525</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p7tcdpryz5hdjfvxh6ofxklnfm">fatcat:p7tcdpryz5hdjfvxh6ofxklnfm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305005928/http://pdfs.semanticscholar.org/e36c/3a7cc3cb46120d0aebc34ddd6d1f7d4b4804.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/e3/6c/e36c3a7cc3cb46120d0aebc34ddd6d1f7d4b4804.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkj163"> <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/PMC1347525" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Straightforward and complete deposition of NMR data to the PDBe

Christopher J. Penkett, Glen van Ginkel, Sameer Velankar, Jawahar Swaminathan, Eldon L. Ulrich, Steve Mading, Tim J. Stevens, Rasmus H. Fogh, Aleksandras Gutmanas, Gerard J. Kleywegt, Kim Henrick, Wim F. Vranken
<span title="2010-08-03">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cimmcbrwkbf4xblwfxyaslsraa" style="color: black;">Journal of Biomolecular NMR</a> </i> &nbsp;
We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB.  ...  This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information  ...  BMRB is supported by grant LM05799 from the US National Library of Medicine.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10858-010-9439-3">doi:10.1007/s10858-010-9439-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20680401">pmid:20680401</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2950272/">pmcid:PMC2950272</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dwh4dfnbavfvdgsnvgp3pemj34">fatcat:dwh4dfnbavfvdgsnvgp3pemj34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726172228/https://link.springer.com/content/pdf/10.1007%2Fs10858-010-9439-3.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/37/41/37416f31c3abc821c5e752a4db79913b2accc7f9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10858-010-9439-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950272" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Parsers, Data Structures and Algorithms for Macromolecular Analysis Toolkit (MAT): Design and Implementation [article]

Gazal Kalyan, Vivek Junghare, S John S, Anupam Chattopadhyay, Pralay Mitra, Saugata Hazra
<span title="2019-04-11">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
MAT provides advanced data structure which is time efficient and is designed to avail reusability and consistency in a systematic framework.  ...  The same data structure is extended to accommodate information from the .mmcif and .mmtf file parsers.  ...  These designed buckets together make up the core data structure to handle the entire information of a protein system.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/605907">doi:10.1101/605907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cerzj5gxcjaurp2webyb4lz674">fatcat:cerzj5gxcjaurp2webyb4lz674</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502100151/https://www.biorxiv.org/content/biorxiv/early/2019/04/13/605907.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/20/77/20770e70cd0b53445efaf122188e46dc409f35cd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/605907"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>
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