APSY-NMR for protein backbone assignment in high-throughput structural biology View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-01

AUTHORS

Samit Kumar Dutta, Pedro Serrano, Andrew Proudfoot, Michael Geralt, Bill Pedrini, Torsten Herrmann, Kurt Wüthrich

ABSTRACT

A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [(1)H,(1)H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination. More... »

PAGES

47-53

References to SciGraph publications

  • 2015-01. NMR structure determination of the protein NP_344798.1 as the first representative of Pfam PF06042 in JOURNAL OF BIOMOLECULAR NMR
  • 2010-04. SAGA: rapid automatic mainchain NMR assignment for large proteins in JOURNAL OF BIOMOLECULAR NMR
  • 2002-11. Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS in JOURNAL OF BIOMOLECULAR NMR
  • 2006-05. Automated Resonance Assignment of Proteins: 6 DAPSY-NMR in JOURNAL OF BIOMOLECULAR NMR
  • 2011-01. Celebrating its 20th anniversary in 2011, the Journal of Biomolecular NMR looks forward to the second decade of the 21st century in JOURNAL OF BIOMOLECULAR NMR
  • 2008-11. APSY-NMR with proteins: practical aspects and backbone assignment in JOURNAL OF BIOMOLECULAR NMR
  • 2008-09. Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY in JOURNAL OF BIOMOLECULAR NMR
  • 2008-05. Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach in JOURNAL OF BIOMOLECULAR NMR
  • 2008-07. Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH in JOURNAL OF BIOMOLECULAR NMR
  • 2009-02. Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm in JOURNAL OF BIOMOLECULAR NMR
  • 2013-10. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins in JOURNAL OF BIOMOLECULAR NMR
  • 2008-10. Assignment of protein NMR spectra based on projections, multi-way decomposition and a fast correlation approach in JOURNAL OF BIOMOLECULAR NMR
  • 2000-06. A tracked approach for automated NMR assignments in proteins (TATAPRO) in JOURNAL OF BIOMOLECULAR NMR
  • 2012-08. The J-UNIO protocol for automated protein structure determination by NMR in solution in JOURNAL OF BIOMOLECULAR NMR
  • 2009-05. Highly automated protein backbone resonance assignment within a few hours: the «BATCH» strategy and software package in JOURNAL OF BIOMOLECULAR NMR
  • 2012-09. TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra in JOURNAL OF BIOMOLECULAR NMR
  • 2015-01. J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4 in JOURNAL OF BIOMOLECULAR NMR
  • 2012-09. Automated protein backbone assignment using the projection-decomposition approach in JOURNAL OF BIOMOLECULAR NMR
  • 2014-11. PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination in JOURNAL OF BIOMOLECULAR NMR
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s10858-014-9881-8

    DOI

    http://dx.doi.org/10.1007/s10858-014-9881-8

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1028626868

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25428764


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biochemistry and Cell Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Nuclear Magnetic Resonance, Biomolecular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Structure, Tertiary", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Software", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Joint Center for Structural Genomics", 
              "id": "https://www.grid.ac/institutes/grid.419677.a", 
              "name": [
                "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, 92037, La Jolla, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Dutta", 
            "givenName": "Samit Kumar", 
            "id": "sg:person.01333664300.46", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333664300.46"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Joint Center for Structural Genomics", 
              "id": "https://www.grid.ac/institutes/grid.419677.a", 
              "name": [
                "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, 92037, La Jolla, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Serrano", 
            "givenName": "Pedro", 
            "id": "sg:person.01050641014.73", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050641014.73"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Joint Center for Structural Genomics", 
              "id": "https://www.grid.ac/institutes/grid.419677.a", 
              "name": [
                "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, 92037, La Jolla, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Proudfoot", 
            "givenName": "Andrew", 
            "id": "sg:person.0656373400.45", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0656373400.45"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Joint Center for Structural Genomics", 
              "id": "https://www.grid.ac/institutes/grid.419677.a", 
              "name": [
                "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, 92037, La Jolla, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Geralt", 
            "givenName": "Michael", 
            "id": "sg:person.0636707533.22", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0636707533.22"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Paul Scherrer Institute", 
              "id": "https://www.grid.ac/institutes/grid.5991.4", 
              "name": [
                "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, 92037, La Jolla, CA, USA", 
                "Institute of Molecular Biology and Biophysics, ETH Z\u00fcrich, 8093, Zurich, Switzerland", 
                "SwissFEL Project, Paul Scherrer Institute (PSI), 5232, Villigen, Switzerland"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Pedrini", 
            "givenName": "Bill", 
            "id": "sg:person.0726342121.54", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0726342121.54"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Analytical Sciences", 
              "id": "https://www.grid.ac/institutes/grid.493282.6", 
              "name": [
                "Institut des Sciences Analytiques, Centre de RMN \u00e0 Tr\u00e8s Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, Universit\u00e9 de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Herrmann", 
            "givenName": "Torsten", 
            "id": "sg:person.01047471377.29", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01047471377.29"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Swiss Federal Institute of Technology in Zurich", 
              "id": "https://www.grid.ac/institutes/grid.5801.c", 
              "name": [
                "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, 92037, La Jolla, CA, USA", 
                "Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA", 
                "Institute of Molecular Biology and Biophysics, ETH Z\u00fcrich, 8093, Zurich, Switzerland"
              ], 
              "type": "Organization"
            }, 
            "familyName": "W\u00fcthrich", 
            "givenName": "Kurt", 
            "id": "sg:person.01242752130.43", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242752130.43"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1002/(sici)1096-987x(19970115)18:1<139::aid-jcc13>3.0.co;2-h", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000128522"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-013-9779-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002638771", 
              "https://doi.org/10.1007/s10858-013-9779-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-008-9291-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003317793", 
              "https://doi.org/10.1007/s10858-008-9291-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jmr.2013.08.010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007451787"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-012-9649-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008947873", 
              "https://doi.org/10.1007/s10858-012-9649-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1008315111278", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010064947", 
              "https://doi.org/10.1023/a:1008315111278"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-012-9645-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011401103", 
              "https://doi.org/10.1007/s10858-012-9645-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1006/jmbi.1997.1284", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011642887"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0022-2836(02)00241-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011905922"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/cbic.201200044", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011944456"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-014-9855-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014811715", 
              "https://doi.org/10.1007/s10858-014-9855-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-014-9855-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014811715", 
              "https://doi.org/10.1007/s10858-014-9855-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1006/jmbi.1997.1052", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016275535"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-012-9652-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017304320", 
              "https://doi.org/10.1007/s10858-012-9652-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.0504818102", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022152168"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-014-9886-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022643269", 
              "https://doi.org/10.1007/s10858-014-9886-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-008-9238-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023469419", 
              "https://doi.org/10.1007/s10858-008-9238-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-008-9266-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026481648", 
              "https://doi.org/10.1007/s10858-008-9266-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-010-9403-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026549200", 
              "https://doi.org/10.1007/s10858-010-9403-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-010-9403-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026549200", 
              "https://doi.org/10.1007/s10858-010-9403-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/0022-2364(76)90028-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030237181"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-014-9878-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030852302", 
              "https://doi.org/10.1007/s10858-014-9878-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/ja305091n", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037057740"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1021614115432", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038114673", 
              "https://doi.org/10.1023/a:1021614115432"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-006-0030-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040911782", 
              "https://doi.org/10.1007/s10858-006-0030-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-010-9466-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044501148", 
              "https://doi.org/10.1007/s10858-010-9466-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-009-9314-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047209886", 
              "https://doi.org/10.1007/s10858-009-9314-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-009-9314-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047209886", 
              "https://doi.org/10.1007/s10858-009-9314-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-008-9265-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047647030", 
              "https://doi.org/10.1007/s10858-008-9265-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-008-9243-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050254287", 
              "https://doi.org/10.1007/s10858-008-9243-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-008-9259-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051160089", 
              "https://doi.org/10.1007/s10858-008-9259-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0076-6879(01)39311-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052118232"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/bip.22348", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053606811"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2015-01", 
        "datePublishedReg": "2015-01-01", 
        "description": "A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [(1)H,(1)H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1007/s10858-014-9881-8", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2699233", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2699217", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1101518", 
            "issn": [
              "0925-2738", 
              "1573-5001"
            ], 
            "name": "Journal of Biomolecular NMR", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "61"
          }
        ], 
        "name": "APSY-NMR for protein backbone assignment in high-throughput structural biology", 
        "pagination": "47-53", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "885ea0318ed348a52fda84fdb1e01f5ab714c09bfa46e7646725922fcb4465c6"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "25428764"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "9110829"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/s10858-014-9881-8"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1028626868"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/s10858-014-9881-8", 
          "https://app.dimensions.ai/details/publication/pub.1028626868"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T15:46", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8664_00000488.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1007/s10858-014-9881-8"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s10858-014-9881-8'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s10858-014-9881-8'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s10858-014-9881-8'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s10858-014-9881-8'


     

    This table displays all metadata directly associated to this object as RDF triples.

    256 TRIPLES      21 PREDICATES      63 URIs      25 LITERALS      13 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/s10858-014-9881-8 schema:about N3330c84e28874e5fba6d6b08ca52e522
    2 N45bd0ab1235a4158a478c079d390a9c3
    3 N6484101668e3434ea73cf028e3d542ab
    4 Ndce2e094b24944b3925272b7e3d996ad
    5 anzsrc-for:06
    6 anzsrc-for:0601
    7 schema:author N6bbdbb7046a24bcfbd7389bb4b2c59bd
    8 schema:citation sg:pub.10.1007/s10858-006-0030-x
    9 sg:pub.10.1007/s10858-008-9238-2
    10 sg:pub.10.1007/s10858-008-9243-5
    11 sg:pub.10.1007/s10858-008-9259-x
    12 sg:pub.10.1007/s10858-008-9265-z
    13 sg:pub.10.1007/s10858-008-9266-y
    14 sg:pub.10.1007/s10858-008-9291-x
    15 sg:pub.10.1007/s10858-009-9314-2
    16 sg:pub.10.1007/s10858-010-9403-2
    17 sg:pub.10.1007/s10858-010-9466-0
    18 sg:pub.10.1007/s10858-012-9645-2
    19 sg:pub.10.1007/s10858-012-9649-y
    20 sg:pub.10.1007/s10858-012-9652-3
    21 sg:pub.10.1007/s10858-013-9779-x
    22 sg:pub.10.1007/s10858-014-9855-x
    23 sg:pub.10.1007/s10858-014-9878-3
    24 sg:pub.10.1007/s10858-014-9886-3
    25 sg:pub.10.1023/a:1008315111278
    26 sg:pub.10.1023/a:1021614115432
    27 https://doi.org/10.1002/(sici)1096-987x(19970115)18:1<139::aid-jcc13>3.0.co;2-h
    28 https://doi.org/10.1002/bip.22348
    29 https://doi.org/10.1002/cbic.201200044
    30 https://doi.org/10.1006/jmbi.1997.1052
    31 https://doi.org/10.1006/jmbi.1997.1284
    32 https://doi.org/10.1016/0022-2364(76)90028-7
    33 https://doi.org/10.1016/j.jmr.2013.08.010
    34 https://doi.org/10.1016/s0022-2836(02)00241-3
    35 https://doi.org/10.1016/s0076-6879(01)39311-4
    36 https://doi.org/10.1021/ja305091n
    37 https://doi.org/10.1073/pnas.0504818102
    38 schema:datePublished 2015-01
    39 schema:datePublishedReg 2015-01-01
    40 schema:description A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [(1)H,(1)H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.
    41 schema:genre research_article
    42 schema:inLanguage en
    43 schema:isAccessibleForFree true
    44 schema:isPartOf N5e7617f186324256824124e53b4538e3
    45 N60b8d8887ef84f2ebd921947ac87581c
    46 sg:journal.1101518
    47 schema:name APSY-NMR for protein backbone assignment in high-throughput structural biology
    48 schema:pagination 47-53
    49 schema:productId N0b20a5d9609f4cad912344202c47cedf
    50 N68726cb5de3b45db8922ea8c362da100
    51 N9327b9f0db0e4805a1cdd1afb30bc0ac
    52 Na82eead1111b4b7ea077e0ff56382e31
    53 Nac321724c5cb4778990260107a7878d3
    54 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028626868
    55 https://doi.org/10.1007/s10858-014-9881-8
    56 schema:sdDatePublished 2019-04-10T15:46
    57 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    58 schema:sdPublisher N187d8b7434d3441aa136ecc3e2d4f472
    59 schema:url http://link.springer.com/10.1007/s10858-014-9881-8
    60 sgo:license sg:explorer/license/
    61 sgo:sdDataset articles
    62 rdf:type schema:ScholarlyArticle
    63 N0b20a5d9609f4cad912344202c47cedf schema:name nlm_unique_id
    64 schema:value 9110829
    65 rdf:type schema:PropertyValue
    66 N187d8b7434d3441aa136ecc3e2d4f472 schema:name Springer Nature - SN SciGraph project
    67 rdf:type schema:Organization
    68 N2ba433a07929441f88c9525ce0024574 rdf:first sg:person.0656373400.45
    69 rdf:rest N726db33cec91498489755a72cb093627
    70 N3330c84e28874e5fba6d6b08ca52e522 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    71 schema:name Protein Structure, Tertiary
    72 rdf:type schema:DefinedTerm
    73 N45bd0ab1235a4158a478c079d390a9c3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    74 schema:name Nuclear Magnetic Resonance, Biomolecular
    75 rdf:type schema:DefinedTerm
    76 N46704d8a643c4e1f8b339e0e7fe61c0a rdf:first sg:person.0726342121.54
    77 rdf:rest N7448606bda564b7289d4686c57a314bc
    78 N5e7617f186324256824124e53b4538e3 schema:volumeNumber 61
    79 rdf:type schema:PublicationVolume
    80 N60b8d8887ef84f2ebd921947ac87581c schema:issueNumber 1
    81 rdf:type schema:PublicationIssue
    82 N6484101668e3434ea73cf028e3d542ab schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    83 schema:name Proteins
    84 rdf:type schema:DefinedTerm
    85 N68726cb5de3b45db8922ea8c362da100 schema:name doi
    86 schema:value 10.1007/s10858-014-9881-8
    87 rdf:type schema:PropertyValue
    88 N6bbdbb7046a24bcfbd7389bb4b2c59bd rdf:first sg:person.01333664300.46
    89 rdf:rest Ndab7a2b5d7ad4dd4ad205056ef70dfd0
    90 N726db33cec91498489755a72cb093627 rdf:first sg:person.0636707533.22
    91 rdf:rest N46704d8a643c4e1f8b339e0e7fe61c0a
    92 N7448606bda564b7289d4686c57a314bc rdf:first sg:person.01047471377.29
    93 rdf:rest Nb6c6de0e7c514cd0970c26954f20b8e4
    94 N9327b9f0db0e4805a1cdd1afb30bc0ac schema:name readcube_id
    95 schema:value 885ea0318ed348a52fda84fdb1e01f5ab714c09bfa46e7646725922fcb4465c6
    96 rdf:type schema:PropertyValue
    97 Na82eead1111b4b7ea077e0ff56382e31 schema:name dimensions_id
    98 schema:value pub.1028626868
    99 rdf:type schema:PropertyValue
    100 Nac321724c5cb4778990260107a7878d3 schema:name pubmed_id
    101 schema:value 25428764
    102 rdf:type schema:PropertyValue
    103 Nb6c6de0e7c514cd0970c26954f20b8e4 rdf:first sg:person.01242752130.43
    104 rdf:rest rdf:nil
    105 Ndab7a2b5d7ad4dd4ad205056ef70dfd0 rdf:first sg:person.01050641014.73
    106 rdf:rest N2ba433a07929441f88c9525ce0024574
    107 Ndce2e094b24944b3925272b7e3d996ad schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    108 schema:name Software
    109 rdf:type schema:DefinedTerm
    110 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    111 schema:name Biological Sciences
    112 rdf:type schema:DefinedTerm
    113 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    114 schema:name Biochemistry and Cell Biology
    115 rdf:type schema:DefinedTerm
    116 sg:grant.2699217 http://pending.schema.org/fundedItem sg:pub.10.1007/s10858-014-9881-8
    117 rdf:type schema:MonetaryGrant
    118 sg:grant.2699233 http://pending.schema.org/fundedItem sg:pub.10.1007/s10858-014-9881-8
    119 rdf:type schema:MonetaryGrant
    120 sg:journal.1101518 schema:issn 0925-2738
    121 1573-5001
    122 schema:name Journal of Biomolecular NMR
    123 rdf:type schema:Periodical
    124 sg:person.01047471377.29 schema:affiliation https://www.grid.ac/institutes/grid.493282.6
    125 schema:familyName Herrmann
    126 schema:givenName Torsten
    127 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01047471377.29
    128 rdf:type schema:Person
    129 sg:person.01050641014.73 schema:affiliation https://www.grid.ac/institutes/grid.419677.a
    130 schema:familyName Serrano
    131 schema:givenName Pedro
    132 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050641014.73
    133 rdf:type schema:Person
    134 sg:person.01242752130.43 schema:affiliation https://www.grid.ac/institutes/grid.5801.c
    135 schema:familyName Wüthrich
    136 schema:givenName Kurt
    137 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242752130.43
    138 rdf:type schema:Person
    139 sg:person.01333664300.46 schema:affiliation https://www.grid.ac/institutes/grid.419677.a
    140 schema:familyName Dutta
    141 schema:givenName Samit Kumar
    142 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333664300.46
    143 rdf:type schema:Person
    144 sg:person.0636707533.22 schema:affiliation https://www.grid.ac/institutes/grid.419677.a
    145 schema:familyName Geralt
    146 schema:givenName Michael
    147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0636707533.22
    148 rdf:type schema:Person
    149 sg:person.0656373400.45 schema:affiliation https://www.grid.ac/institutes/grid.419677.a
    150 schema:familyName Proudfoot
    151 schema:givenName Andrew
    152 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0656373400.45
    153 rdf:type schema:Person
    154 sg:person.0726342121.54 schema:affiliation https://www.grid.ac/institutes/grid.5991.4
    155 schema:familyName Pedrini
    156 schema:givenName Bill
    157 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0726342121.54
    158 rdf:type schema:Person
    159 sg:pub.10.1007/s10858-006-0030-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1040911782
    160 https://doi.org/10.1007/s10858-006-0030-x
    161 rdf:type schema:CreativeWork
    162 sg:pub.10.1007/s10858-008-9238-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023469419
    163 https://doi.org/10.1007/s10858-008-9238-2
    164 rdf:type schema:CreativeWork
    165 sg:pub.10.1007/s10858-008-9243-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050254287
    166 https://doi.org/10.1007/s10858-008-9243-5
    167 rdf:type schema:CreativeWork
    168 sg:pub.10.1007/s10858-008-9259-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1051160089
    169 https://doi.org/10.1007/s10858-008-9259-x
    170 rdf:type schema:CreativeWork
    171 sg:pub.10.1007/s10858-008-9265-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1047647030
    172 https://doi.org/10.1007/s10858-008-9265-z
    173 rdf:type schema:CreativeWork
    174 sg:pub.10.1007/s10858-008-9266-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1026481648
    175 https://doi.org/10.1007/s10858-008-9266-y
    176 rdf:type schema:CreativeWork
    177 sg:pub.10.1007/s10858-008-9291-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1003317793
    178 https://doi.org/10.1007/s10858-008-9291-x
    179 rdf:type schema:CreativeWork
    180 sg:pub.10.1007/s10858-009-9314-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047209886
    181 https://doi.org/10.1007/s10858-009-9314-2
    182 rdf:type schema:CreativeWork
    183 sg:pub.10.1007/s10858-010-9403-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026549200
    184 https://doi.org/10.1007/s10858-010-9403-2
    185 rdf:type schema:CreativeWork
    186 sg:pub.10.1007/s10858-010-9466-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044501148
    187 https://doi.org/10.1007/s10858-010-9466-0
    188 rdf:type schema:CreativeWork
    189 sg:pub.10.1007/s10858-012-9645-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011401103
    190 https://doi.org/10.1007/s10858-012-9645-2
    191 rdf:type schema:CreativeWork
    192 sg:pub.10.1007/s10858-012-9649-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1008947873
    193 https://doi.org/10.1007/s10858-012-9649-y
    194 rdf:type schema:CreativeWork
    195 sg:pub.10.1007/s10858-012-9652-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017304320
    196 https://doi.org/10.1007/s10858-012-9652-3
    197 rdf:type schema:CreativeWork
    198 sg:pub.10.1007/s10858-013-9779-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1002638771
    199 https://doi.org/10.1007/s10858-013-9779-x
    200 rdf:type schema:CreativeWork
    201 sg:pub.10.1007/s10858-014-9855-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1014811715
    202 https://doi.org/10.1007/s10858-014-9855-x
    203 rdf:type schema:CreativeWork
    204 sg:pub.10.1007/s10858-014-9878-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030852302
    205 https://doi.org/10.1007/s10858-014-9878-3
    206 rdf:type schema:CreativeWork
    207 sg:pub.10.1007/s10858-014-9886-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022643269
    208 https://doi.org/10.1007/s10858-014-9886-3
    209 rdf:type schema:CreativeWork
    210 sg:pub.10.1023/a:1008315111278 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010064947
    211 https://doi.org/10.1023/a:1008315111278
    212 rdf:type schema:CreativeWork
    213 sg:pub.10.1023/a:1021614115432 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038114673
    214 https://doi.org/10.1023/a:1021614115432
    215 rdf:type schema:CreativeWork
    216 https://doi.org/10.1002/(sici)1096-987x(19970115)18:1<139::aid-jcc13>3.0.co;2-h schema:sameAs https://app.dimensions.ai/details/publication/pub.1000128522
    217 rdf:type schema:CreativeWork
    218 https://doi.org/10.1002/bip.22348 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053606811
    219 rdf:type schema:CreativeWork
    220 https://doi.org/10.1002/cbic.201200044 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011944456
    221 rdf:type schema:CreativeWork
    222 https://doi.org/10.1006/jmbi.1997.1052 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016275535
    223 rdf:type schema:CreativeWork
    224 https://doi.org/10.1006/jmbi.1997.1284 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011642887
    225 rdf:type schema:CreativeWork
    226 https://doi.org/10.1016/0022-2364(76)90028-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030237181
    227 rdf:type schema:CreativeWork
    228 https://doi.org/10.1016/j.jmr.2013.08.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007451787
    229 rdf:type schema:CreativeWork
    230 https://doi.org/10.1016/s0022-2836(02)00241-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011905922
    231 rdf:type schema:CreativeWork
    232 https://doi.org/10.1016/s0076-6879(01)39311-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052118232
    233 rdf:type schema:CreativeWork
    234 https://doi.org/10.1021/ja305091n schema:sameAs https://app.dimensions.ai/details/publication/pub.1037057740
    235 rdf:type schema:CreativeWork
    236 https://doi.org/10.1073/pnas.0504818102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022152168
    237 rdf:type schema:CreativeWork
    238 https://www.grid.ac/institutes/grid.419677.a schema:alternateName Joint Center for Structural Genomics
    239 schema:name Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA
    240 Joint Center for Structural Genomics, 92037, La Jolla, CA, USA
    241 rdf:type schema:Organization
    242 https://www.grid.ac/institutes/grid.493282.6 schema:alternateName Institute of Analytical Sciences
    243 schema:name Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
    244 rdf:type schema:Organization
    245 https://www.grid.ac/institutes/grid.5801.c schema:alternateName Swiss Federal Institute of Technology in Zurich
    246 schema:name Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA
    247 Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
    248 Joint Center for Structural Genomics, 92037, La Jolla, CA, USA
    249 Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA
    250 rdf:type schema:Organization
    251 https://www.grid.ac/institutes/grid.5991.4 schema:alternateName Paul Scherrer Institute
    252 schema:name Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, CA, USA
    253 Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
    254 Joint Center for Structural Genomics, 92037, La Jolla, CA, USA
    255 SwissFEL Project, Paul Scherrer Institute (PSI), 5232, Villigen, Switzerland
    256 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...