The J-UNIO protocol for automated protein structure determination by NMR in solution View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-08

AUTHORS

Pedro Serrano, Bill Pedrini, Biswaranjan Mohanty, Michael Geralt, Torsten Herrmann, Kurt Wüthrich

ABSTRACT

The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [(1)H,(1)H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6-10 days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP_926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluated. More... »

PAGES

341-354

References to SciGraph publications

  • 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
  • 2005-12. Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS
  • 2008-11. APSY-NMR with proteins: practical aspects and backbone assignment in JOURNAL OF BIOMOLECULAR NMR
  • 1992-03. Assessment of protein models with three-dimensional profiles in NATURE
  • 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
  • 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
  • 2011-06. Exclusively NOESY-based automated NMR assignment and structure determination of proteins 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
  • 1994-03. The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data 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
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s10858-012-9645-2

    DOI

    http://dx.doi.org/10.1007/s10858-012-9645-2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1011401103

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22752932


    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": "Amino Acid Sequence", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Bacterial Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Models, Molecular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Molecular Sequence Data", 
            "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 Conformation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Shewanella", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Software", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Solutions", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Joint Center for Structural Genomics", 
              "id": "https://www.grid.ac/institutes/grid.419677.a", 
              "name": [
                "Department of Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, The Scripps Research Institute, 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": "Paul Scherrer Institute", 
              "id": "https://www.grid.ac/institutes/grid.5991.4", 
              "name": [
                "Department of Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA", 
                "Institute of Molecular Biology and Biophysics, ETH Z\u00fcrich, Schafmattstrasse 20, 8093, Zurich, Switzerland", 
                "SwissFEL Project, Paul Scherrer Institute, 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": "Monash University", 
              "id": "https://www.grid.ac/institutes/grid.1002.3", 
              "name": [
                "Department of Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, The Scripps Research Institute, 92037, La Jolla, CA, USA", 
                "Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Campus, 381 Royal Parade, 3052, Parkville, VIC, Australia"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mohanty", 
            "givenName": "Biswaranjan", 
            "id": "sg:person.0705361744.54", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0705361744.54"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Joint Center for Structural Genomics", 
              "id": "https://www.grid.ac/institutes/grid.419677.a", 
              "name": [
                "Department of Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, The Scripps Research Institute, 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": "Claude Bernard University Lyon 1", 
              "id": "https://www.grid.ac/institutes/grid.7849.2", 
              "name": [
                "Centre de RMN \u00e0 Tr\u00e8s Hauts Champs, Universit\u00e9 de Lyon, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, 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 Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA", 
                "Skaggs Institute for Chemical Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA", 
                "Joint Center for Structural Genomics, The Scripps Research Institute, 92037, La Jolla, CA, USA", 
                "Institute of Molecular Biology and Biophysics, ETH Z\u00fcrich, Schafmattstrasse 20, 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/s10969-005-9000-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000472843", 
              "https://doi.org/10.1007/s10969-005-9000-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10969-005-9000-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000472843", 
              "https://doi.org/10.1007/s10969-005-9000-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/10.1107/s0021889892009944", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003451988"
            ], 
            "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/bf00175245", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010505080", 
              "https://doi.org/10.1007/bf00175245"
            ], 
            "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/10.1107/s1744309110033658", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011988470"
            ], 
            "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.10.1038/356083a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017646872", 
              "https://doi.org/10.1038/356083a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1107/s1744309110038212", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021055198"
            ], 
            "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/s10858-008-9238-2", 
            "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/10.1016/0022-2836(94)90042-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027065301"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/0263-7855(96)00009-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028069795"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1107/s1744309110030320", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029095754"
            ], 
            "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/s10858-011-9502-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030537043", 
              "https://doi.org/10.1007/s10858-011-9502-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1107/s1744309110005890", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034475717"
            ], 
            "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": "https://doi.org/10.1107/s1744309110020956", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041949117"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.0408490102", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043217316"
            ], 
            "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": "https://doi.org/10.1073/pnas.142413399", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048803315"
            ], 
            "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/10.1021/bi00213a010", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1055165526"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2012-08", 
        "datePublishedReg": "2012-08-01", 
        "description": "The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [(1)H,(1)H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6-10 days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP_926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluated.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1007/s10858-012-9645-2", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2699233", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.5208744", 
            "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": "4", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "53"
          }
        ], 
        "name": "The J-UNIO protocol for automated protein structure determination by NMR in solution", 
        "pagination": "341-354", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "3651a18998cf5cb7f040f49c2911670ac1dc2830b672f4a921cf956d970027e5"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "22752932"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "9110829"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/s10858-012-9645-2"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1011401103"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/s10858-012-9645-2", 
          "https://app.dimensions.ai/details/publication/pub.1011401103"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T17:25", 
        "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_8672_00000486.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1007/s10858-012-9645-2"
      }
    ]
     

    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/s10858-012-9645-2'

    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/s10858-012-9645-2'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s10858-012-9645-2'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s10858-012-9645-2'


     

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

    280 TRIPLES      21 PREDICATES      71 URIs      31 LITERALS      19 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/s10858-012-9645-2 schema:about N22ca59e4d7ac4f3f8161237292b0671f
    2 N325689b4b62f424184d4663fe642bee2
    3 N4a306954ee794704b7b300091fdddff9
    4 N4fba4b0968c94f59b349fa8504777a20
    5 N579067dae5384ff3abea1a1483e5f82f
    6 N6734a28ce4e3442086e7681e2b0ea4e6
    7 N71969a859b0c409792e2583cd3f846d9
    8 N83a58403338d4974ba8a4384a31086bc
    9 Ne4a9a6235a6e47828fd8cbb54e016d62
    10 Nf0b34827484840a99082fac75237a699
    11 anzsrc-for:06
    12 anzsrc-for:0601
    13 schema:author N0d0364b61c04433497950c866d3a3820
    14 schema:citation sg:pub.10.1007/bf00175245
    15 sg:pub.10.1007/s10858-008-9238-2
    16 sg:pub.10.1007/s10858-008-9243-5
    17 sg:pub.10.1007/s10858-008-9259-x
    18 sg:pub.10.1007/s10858-008-9265-z
    19 sg:pub.10.1007/s10858-008-9266-y
    20 sg:pub.10.1007/s10858-008-9291-x
    21 sg:pub.10.1007/s10858-009-9314-2
    22 sg:pub.10.1007/s10858-010-9403-2
    23 sg:pub.10.1007/s10858-011-9502-8
    24 sg:pub.10.1007/s10969-005-9000-x
    25 sg:pub.10.1023/a:1008315111278
    26 sg:pub.10.1023/a:1021614115432
    27 sg:pub.10.1038/356083a0
    28 https://doi.org/10.1002/(sici)1096-987x(19970115)18:1<139::aid-jcc13>3.0.co;2-h
    29 https://doi.org/10.1006/jmbi.1997.1052
    30 https://doi.org/10.1006/jmbi.1997.1284
    31 https://doi.org/10.1016/0022-2364(76)90028-7
    32 https://doi.org/10.1016/0022-2836(94)90042-6
    33 https://doi.org/10.1016/0263-7855(96)00009-4
    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/bi00213a010
    37 https://doi.org/10.1073/pnas.0408490102
    38 https://doi.org/10.1073/pnas.0504818102
    39 https://doi.org/10.1073/pnas.142413399
    40 https://doi.org/10.1107/s0021889892009944
    41 https://doi.org/10.1107/s1744309110005890
    42 https://doi.org/10.1107/s1744309110020956
    43 https://doi.org/10.1107/s1744309110030320
    44 https://doi.org/10.1107/s1744309110033658
    45 https://doi.org/10.1107/s1744309110038212
    46 schema:datePublished 2012-08
    47 schema:datePublishedReg 2012-08-01
    48 schema:description The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [(1)H,(1)H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6-10 days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP_926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluated.
    49 schema:genre research_article
    50 schema:inLanguage en
    51 schema:isAccessibleForFree true
    52 schema:isPartOf Nb81b94ffbd7e4d019f3e55fbede7ebf7
    53 Nbde8325572b44bd594deb42c6f692256
    54 sg:journal.1101518
    55 schema:name The J-UNIO protocol for automated protein structure determination by NMR in solution
    56 schema:pagination 341-354
    57 schema:productId N1d05d48bcd6c48008aa10cf5126e80b4
    58 N3d24b74306d94a51b6563259f6497a0e
    59 N875b26c6c14c492c86899d111377f2db
    60 Na17386fc30bd48d8a07c1360ee81dff9
    61 Naa81529df4a6429e861d0ba035633a8f
    62 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011401103
    63 https://doi.org/10.1007/s10858-012-9645-2
    64 schema:sdDatePublished 2019-04-10T17:25
    65 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    66 schema:sdPublisher Nc7aa879191c3413f94345d081fb30a3f
    67 schema:url http://link.springer.com/10.1007/s10858-012-9645-2
    68 sgo:license sg:explorer/license/
    69 sgo:sdDataset articles
    70 rdf:type schema:ScholarlyArticle
    71 N0d0364b61c04433497950c866d3a3820 rdf:first sg:person.01050641014.73
    72 rdf:rest Nee0a327812ce42f093448afdbf55a4ee
    73 N1d05d48bcd6c48008aa10cf5126e80b4 schema:name dimensions_id
    74 schema:value pub.1011401103
    75 rdf:type schema:PropertyValue
    76 N22ca59e4d7ac4f3f8161237292b0671f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    77 schema:name Molecular Sequence Data
    78 rdf:type schema:DefinedTerm
    79 N325689b4b62f424184d4663fe642bee2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    80 schema:name Models, Molecular
    81 rdf:type schema:DefinedTerm
    82 N3d24b74306d94a51b6563259f6497a0e schema:name readcube_id
    83 schema:value 3651a18998cf5cb7f040f49c2911670ac1dc2830b672f4a921cf956d970027e5
    84 rdf:type schema:PropertyValue
    85 N4a306954ee794704b7b300091fdddff9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    86 schema:name Bacterial Proteins
    87 rdf:type schema:DefinedTerm
    88 N4fba4b0968c94f59b349fa8504777a20 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    89 schema:name Nuclear Magnetic Resonance, Biomolecular
    90 rdf:type schema:DefinedTerm
    91 N579067dae5384ff3abea1a1483e5f82f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    92 schema:name Proteins
    93 rdf:type schema:DefinedTerm
    94 N6734a28ce4e3442086e7681e2b0ea4e6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    95 schema:name Amino Acid Sequence
    96 rdf:type schema:DefinedTerm
    97 N71969a859b0c409792e2583cd3f846d9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    98 schema:name Shewanella
    99 rdf:type schema:DefinedTerm
    100 N83a58403338d4974ba8a4384a31086bc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    101 schema:name Protein Conformation
    102 rdf:type schema:DefinedTerm
    103 N875b26c6c14c492c86899d111377f2db schema:name doi
    104 schema:value 10.1007/s10858-012-9645-2
    105 rdf:type schema:PropertyValue
    106 Na17386fc30bd48d8a07c1360ee81dff9 schema:name pubmed_id
    107 schema:value 22752932
    108 rdf:type schema:PropertyValue
    109 Naa81529df4a6429e861d0ba035633a8f schema:name nlm_unique_id
    110 schema:value 9110829
    111 rdf:type schema:PropertyValue
    112 Nb81b94ffbd7e4d019f3e55fbede7ebf7 schema:issueNumber 4
    113 rdf:type schema:PublicationIssue
    114 Nbde8325572b44bd594deb42c6f692256 schema:volumeNumber 53
    115 rdf:type schema:PublicationVolume
    116 Nbe98a26e837c47ca8d5f68c23e47dd0b rdf:first sg:person.01242752130.43
    117 rdf:rest rdf:nil
    118 Nc57e6b1bf0bc4d8389414e0954b0a9f7 rdf:first sg:person.0636707533.22
    119 rdf:rest Nf1097d59310a4465bd5549457cbfbe21
    120 Nc7aa879191c3413f94345d081fb30a3f schema:name Springer Nature - SN SciGraph project
    121 rdf:type schema:Organization
    122 Ne4a9a6235a6e47828fd8cbb54e016d62 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    123 schema:name Solutions
    124 rdf:type schema:DefinedTerm
    125 Nedc181d4e6ed423ab13a24cadc10b157 rdf:first sg:person.0705361744.54
    126 rdf:rest Nc57e6b1bf0bc4d8389414e0954b0a9f7
    127 Nee0a327812ce42f093448afdbf55a4ee rdf:first sg:person.0726342121.54
    128 rdf:rest Nedc181d4e6ed423ab13a24cadc10b157
    129 Nf0b34827484840a99082fac75237a699 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    130 schema:name Software
    131 rdf:type schema:DefinedTerm
    132 Nf1097d59310a4465bd5549457cbfbe21 rdf:first sg:person.01047471377.29
    133 rdf:rest Nbe98a26e837c47ca8d5f68c23e47dd0b
    134 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    135 schema:name Biological Sciences
    136 rdf:type schema:DefinedTerm
    137 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    138 schema:name Biochemistry and Cell Biology
    139 rdf:type schema:DefinedTerm
    140 sg:grant.2699217 http://pending.schema.org/fundedItem sg:pub.10.1007/s10858-012-9645-2
    141 rdf:type schema:MonetaryGrant
    142 sg:grant.2699233 http://pending.schema.org/fundedItem sg:pub.10.1007/s10858-012-9645-2
    143 rdf:type schema:MonetaryGrant
    144 sg:grant.5208744 http://pending.schema.org/fundedItem sg:pub.10.1007/s10858-012-9645-2
    145 rdf:type schema:MonetaryGrant
    146 sg:journal.1101518 schema:issn 0925-2738
    147 1573-5001
    148 schema:name Journal of Biomolecular NMR
    149 rdf:type schema:Periodical
    150 sg:person.01047471377.29 schema:affiliation https://www.grid.ac/institutes/grid.7849.2
    151 schema:familyName Herrmann
    152 schema:givenName Torsten
    153 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01047471377.29
    154 rdf:type schema:Person
    155 sg:person.01050641014.73 schema:affiliation https://www.grid.ac/institutes/grid.419677.a
    156 schema:familyName Serrano
    157 schema:givenName Pedro
    158 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050641014.73
    159 rdf:type schema:Person
    160 sg:person.01242752130.43 schema:affiliation https://www.grid.ac/institutes/grid.5801.c
    161 schema:familyName Wüthrich
    162 schema:givenName Kurt
    163 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01242752130.43
    164 rdf:type schema:Person
    165 sg:person.0636707533.22 schema:affiliation https://www.grid.ac/institutes/grid.419677.a
    166 schema:familyName Geralt
    167 schema:givenName Michael
    168 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0636707533.22
    169 rdf:type schema:Person
    170 sg:person.0705361744.54 schema:affiliation https://www.grid.ac/institutes/grid.1002.3
    171 schema:familyName Mohanty
    172 schema:givenName Biswaranjan
    173 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0705361744.54
    174 rdf:type schema:Person
    175 sg:person.0726342121.54 schema:affiliation https://www.grid.ac/institutes/grid.5991.4
    176 schema:familyName Pedrini
    177 schema:givenName Bill
    178 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0726342121.54
    179 rdf:type schema:Person
    180 sg:pub.10.1007/bf00175245 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010505080
    181 https://doi.org/10.1007/bf00175245
    182 rdf:type schema:CreativeWork
    183 sg:pub.10.1007/s10858-008-9238-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023469419
    184 https://doi.org/10.1007/s10858-008-9238-2
    185 rdf:type schema:CreativeWork
    186 sg:pub.10.1007/s10858-008-9243-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050254287
    187 https://doi.org/10.1007/s10858-008-9243-5
    188 rdf:type schema:CreativeWork
    189 sg:pub.10.1007/s10858-008-9259-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1051160089
    190 https://doi.org/10.1007/s10858-008-9259-x
    191 rdf:type schema:CreativeWork
    192 sg:pub.10.1007/s10858-008-9265-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1047647030
    193 https://doi.org/10.1007/s10858-008-9265-z
    194 rdf:type schema:CreativeWork
    195 sg:pub.10.1007/s10858-008-9266-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1026481648
    196 https://doi.org/10.1007/s10858-008-9266-y
    197 rdf:type schema:CreativeWork
    198 sg:pub.10.1007/s10858-008-9291-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1003317793
    199 https://doi.org/10.1007/s10858-008-9291-x
    200 rdf:type schema:CreativeWork
    201 sg:pub.10.1007/s10858-009-9314-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047209886
    202 https://doi.org/10.1007/s10858-009-9314-2
    203 rdf:type schema:CreativeWork
    204 sg:pub.10.1007/s10858-010-9403-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026549200
    205 https://doi.org/10.1007/s10858-010-9403-2
    206 rdf:type schema:CreativeWork
    207 sg:pub.10.1007/s10858-011-9502-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030537043
    208 https://doi.org/10.1007/s10858-011-9502-8
    209 rdf:type schema:CreativeWork
    210 sg:pub.10.1007/s10969-005-9000-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1000472843
    211 https://doi.org/10.1007/s10969-005-9000-x
    212 rdf:type schema:CreativeWork
    213 sg:pub.10.1023/a:1008315111278 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010064947
    214 https://doi.org/10.1023/a:1008315111278
    215 rdf:type schema:CreativeWork
    216 sg:pub.10.1023/a:1021614115432 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038114673
    217 https://doi.org/10.1023/a:1021614115432
    218 rdf:type schema:CreativeWork
    219 sg:pub.10.1038/356083a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017646872
    220 https://doi.org/10.1038/356083a0
    221 rdf:type schema:CreativeWork
    222 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
    223 rdf:type schema:CreativeWork
    224 https://doi.org/10.1006/jmbi.1997.1052 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016275535
    225 rdf:type schema:CreativeWork
    226 https://doi.org/10.1006/jmbi.1997.1284 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011642887
    227 rdf:type schema:CreativeWork
    228 https://doi.org/10.1016/0022-2364(76)90028-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030237181
    229 rdf:type schema:CreativeWork
    230 https://doi.org/10.1016/0022-2836(94)90042-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027065301
    231 rdf:type schema:CreativeWork
    232 https://doi.org/10.1016/0263-7855(96)00009-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028069795
    233 rdf:type schema:CreativeWork
    234 https://doi.org/10.1016/s0022-2836(02)00241-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011905922
    235 rdf:type schema:CreativeWork
    236 https://doi.org/10.1016/s0076-6879(01)39311-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052118232
    237 rdf:type schema:CreativeWork
    238 https://doi.org/10.1021/bi00213a010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055165526
    239 rdf:type schema:CreativeWork
    240 https://doi.org/10.1073/pnas.0408490102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043217316
    241 rdf:type schema:CreativeWork
    242 https://doi.org/10.1073/pnas.0504818102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022152168
    243 rdf:type schema:CreativeWork
    244 https://doi.org/10.1073/pnas.142413399 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048803315
    245 rdf:type schema:CreativeWork
    246 https://doi.org/10.1107/s0021889892009944 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003451988
    247 rdf:type schema:CreativeWork
    248 https://doi.org/10.1107/s1744309110005890 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034475717
    249 rdf:type schema:CreativeWork
    250 https://doi.org/10.1107/s1744309110020956 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041949117
    251 rdf:type schema:CreativeWork
    252 https://doi.org/10.1107/s1744309110030320 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029095754
    253 rdf:type schema:CreativeWork
    254 https://doi.org/10.1107/s1744309110033658 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011988470
    255 rdf:type schema:CreativeWork
    256 https://doi.org/10.1107/s1744309110038212 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021055198
    257 rdf:type schema:CreativeWork
    258 https://www.grid.ac/institutes/grid.1002.3 schema:alternateName Monash University
    259 schema:name Department of Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA
    260 Joint Center for Structural Genomics, The Scripps Research Institute, 92037, La Jolla, CA, USA
    261 Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Campus, 381 Royal Parade, 3052, Parkville, VIC, Australia
    262 rdf:type schema:Organization
    263 https://www.grid.ac/institutes/grid.419677.a schema:alternateName Joint Center for Structural Genomics
    264 schema:name Department of Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA
    265 Joint Center for Structural Genomics, The Scripps Research Institute, 92037, La Jolla, CA, USA
    266 rdf:type schema:Organization
    267 https://www.grid.ac/institutes/grid.5801.c schema:alternateName Swiss Federal Institute of Technology in Zurich
    268 schema:name Department of Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA
    269 Institute of Molecular Biology and Biophysics, ETH Zürich, Schafmattstrasse 20, 8093, Zurich, Switzerland
    270 Joint Center for Structural Genomics, The Scripps Research Institute, 92037, La Jolla, CA, USA
    271 Skaggs Institute for Chemical Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA
    272 rdf:type schema:Organization
    273 https://www.grid.ac/institutes/grid.5991.4 schema:alternateName Paul Scherrer Institute
    274 schema:name Department of Molecular Biology, The Scripps Research Institute, 92037, La Jolla, CA, USA
    275 Institute of Molecular Biology and Biophysics, ETH Zürich, Schafmattstrasse 20, 8093, Zurich, Switzerland
    276 SwissFEL Project, Paul Scherrer Institute, 5232, Villigen, Switzerland
    277 rdf:type schema:Organization
    278 https://www.grid.ac/institutes/grid.7849.2 schema:alternateName Claude Bernard University Lyon 1
    279 schema:name Centre de RMN à Très Hauts Champs, Université de Lyon, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France
    280 rdf:type schema:Organization
     




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


    ...