Combined automated NOE assignment and structure calculation with CYANA View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2015-08

AUTHORS

Peter Güntert, Lena Buchner

ABSTRACT

The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR. More... »

PAGES

453-471

References to SciGraph publications

  • 1994-09. NMR View: A computer program for the visualization and analysis of NMR data in JOURNAL OF BIOMOLECULAR NMR
  • 1993-09. The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination in JOURNAL OF BIOMOLECULAR NMR
  • 2015-05. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA in JOURNAL OF BIOMOLECULAR NMR
  • 2009-02. Automated structure determination from NMR spectra in EUROPEAN BIOPHYSICS JOURNAL
  • 2011-06. Exclusively NOESY-based automated NMR assignment and structure determination of proteins in JOURNAL OF BIOMOLECULAR NMR
  • 1997-12. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination in JOURNAL OF BIOMOLECULAR NMR
  • 2003-06. Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS
  • 1995-07. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules in JOURNAL OF BIOMOLECULAR NMR
  • 2014-07. Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta in JOURNAL OF BIOMOLECULAR NMR
  • 2002-08. Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE) in JOURNAL OF BIOMOLECULAR NMR
  • 2011-12. Objective identification of residue ranges for the superposition of protein structures in BMC BIOINFORMATICS
  • 1992-11. Processing of multi-dimensional NMR data with the new software PROSA in JOURNAL OF BIOMOLECULAR NMR
  • 2012-04. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space 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
  • 2012-10. Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2013-11. Stereospecific assignments in proteins using exact NOEs 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
  • 2013-03. Peakmatch: a simple and robust method for peak list matching in JOURNAL OF BIOMOLECULAR NMR
  • 2007-09. KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies in JOURNAL OF BIOMOLECULAR NMR
  • 2009-03. Automated protein structure calculation from NMR data in JOURNAL OF BIOMOLECULAR NMR
  • 2002-10. A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics in JOURNAL OF BIOMOLECULAR NMR
  • 2006-03. Optimal isotope labelling for NMR protein structure determinations in NATURE
  • 2009-09. CASD-NMR: critical assessment of automated structure determination by NMR in NATURE METHODS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s10858-015-9924-9

    DOI

    http://dx.doi.org/10.1007/s10858-015-9924-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1042177174

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25801209


    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": "Algorithms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Models, Molecular", 
            "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": "Software", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Tokyo Metropolitan University", 
              "id": "https://www.grid.ac/institutes/grid.265074.2", 
              "name": [
                "Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany", 
                "Laboratory of Physical Chemistry, ETH Z\u00fcrich, Zurich, Switzerland", 
                "Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "G\u00fcntert", 
            "givenName": "Peter", 
            "id": "sg:person.01201353333.77", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201353333.77"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Goethe University Frankfurt", 
              "id": "https://www.grid.ac/institutes/grid.7839.5", 
              "name": [
                "Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Buchner", 
            "givenName": "Lena", 
            "id": "sg:person.01143034530.91", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01143034530.91"
            ], 
            "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": "https://doi.org/10.1021/ja061136l", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002363078"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/ja061136l", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002363078"
            ], 
            "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.10.1023/a:1026122726574", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004234144", 
              "https://doi.org/10.1023/a:1026122726574"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00404272", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004332552", 
              "https://doi.org/10.1007/bf00404272"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00404272", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004332552", 
              "https://doi.org/10.1007/bf00404272"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.str.2012.01.002", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004887871"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/0022-2836(91)90755-u", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005616750"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1020279503261", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008990540", 
              "https://doi.org/10.1023/a:1020279503261"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-12-170", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010022232", 
              "https://doi.org/10.1186/1471-2105-12-170"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-12-170", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010022232", 
              "https://doi.org/10.1186/1471-2105-12-170"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nsmb.2355", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010043458", 
              "https://doi.org/10.1038/nsmb.2355"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00249-008-0367-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010435591", 
              "https://doi.org/10.1007/s00249-008-0367-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00249-008-0367-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010435591", 
              "https://doi.org/10.1007/s00249-008-0367-z"
            ], 
            "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": "sg:pub.10.1007/s10858-015-9921-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012002218", 
              "https://doi.org/10.1007/s10858-015-9921-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btl589", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012374959"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1107/s1399004714026662", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014436414"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00417486", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015332811", 
              "https://doi.org/10.1007/bf00417486"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00417486", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015332811", 
              "https://doi.org/10.1007/bf00417486"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-013-9708-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015496408", 
              "https://doi.org/10.1007/s10858-013-9708-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-014-9832-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016735616", 
              "https://doi.org/10.1007/s10858-014-9832-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf02192850", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018314375", 
              "https://doi.org/10.1007/bf02192850"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf02192850", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018314375", 
              "https://doi.org/10.1007/bf02192850"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature04525", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019716667", 
              "https://doi.org/10.1038/nature04525"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature04525", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019716667", 
              "https://doi.org/10.1038/nature04525"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature04525", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019716667", 
              "https://doi.org/10.1038/nature04525"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-012-9615-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020000034", 
              "https://doi.org/10.1007/s10858-012-9615-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00174613", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020274348", 
              "https://doi.org/10.1007/bf00174613"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-013-9780-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022005008", 
              "https://doi.org/10.1007/s10858-013-9780-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1006/jmbi.1994.0053", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022908229"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/anie.201408598", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023290329"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1006/jmbi.1997.1044", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023394964"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkm957", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025566031"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-007-9175-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026134817", 
              "https://doi.org/10.1007/s10858-007-9175-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1020997118364", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028389314", 
              "https://doi.org/10.1023/a:1020997118364"
            ], 
            "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": "sg:pub.10.1038/nmeth0909-625", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032293100", 
              "https://doi.org/10.1038/nmeth0909-625"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth0909-625", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032293100", 
              "https://doi.org/10.1038/nmeth0909-625"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1018383106236", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032527294", 
              "https://doi.org/10.1023/a:1018383106236"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/28.1.235", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035055456"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/0022-2836(85)90134-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035083567"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/0022-2836(91)90754-t", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036024947"
            ], 
            "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": "https://doi.org/10.1006/jmbi.1995.0631", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038786017"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.str.2014.11.014", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039036820"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10858-008-9295-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044926556", 
              "https://doi.org/10.1007/s10858-008-9295-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/prot.20820", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051962266"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/prot.20820", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051962266"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1017/s0033583510000326", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1054060929"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1017/s0033583598003436", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1054077673"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1017/s0033583598003436", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1054077673"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/ja049786h", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1055838207"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1021/ja049786h", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1055838207"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2015-08", 
        "datePublishedReg": "2015-08-01", 
        "description": "The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR. ", 
        "genre": "research_article", 
        "id": "sg:pub.10.1007/s10858-015-9924-9", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": false, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.6119203", 
            "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": "62"
          }
        ], 
        "name": "Combined automated NOE assignment and structure calculation with CYANA", 
        "pagination": "453-471", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "c8e97e06e0eb6da3ec7271c31d7a6ee89a5b19cffd17df5e03280fa3fa48178a"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "25801209"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "9110829"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/s10858-015-9924-9"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1042177174"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/s10858-015-9924-9", 
          "https://app.dimensions.ai/details/publication/pub.1042177174"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T23:19", 
        "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_8693_00000490.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1007/s10858-015-9924-9"
      }
    ]
     

    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/s10858-015-9924-9'

    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/s10858-015-9924-9'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s10858-015-9924-9'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s10858-015-9924-9'


     

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

    265 TRIPLES      21 PREDICATES      80 URIs      27 LITERALS      15 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/s10858-015-9924-9 schema:about N174b5c4459624e538f8cd36f3d507357
    2 N35b25c421fc94ec3bb2dccdecbff2882
    3 N4513ed9235624a108bad846cfae3ddd4
    4 N54dbae7321fe4073bb9e8432512f62f9
    5 N8be35a2421e34716ad048aaf14fb9624
    6 N8eece340fecb4a609bf3861ba0038736
    7 anzsrc-for:06
    8 anzsrc-for:0601
    9 schema:author N7c7c2593237e413d90c318e5066b60de
    10 schema:citation sg:pub.10.1007/bf00174613
    11 sg:pub.10.1007/bf00404272
    12 sg:pub.10.1007/bf00417486
    13 sg:pub.10.1007/bf02192850
    14 sg:pub.10.1007/s00249-008-0367-z
    15 sg:pub.10.1007/s10858-007-9175-5
    16 sg:pub.10.1007/s10858-008-9295-6
    17 sg:pub.10.1007/s10858-011-9502-8
    18 sg:pub.10.1007/s10858-012-9615-8
    19 sg:pub.10.1007/s10858-013-9708-z
    20 sg:pub.10.1007/s10858-013-9779-x
    21 sg:pub.10.1007/s10858-013-9780-4
    22 sg:pub.10.1007/s10858-014-9832-4
    23 sg:pub.10.1007/s10858-015-9921-z
    24 sg:pub.10.1023/a:1018383106236
    25 sg:pub.10.1023/a:1020279503261
    26 sg:pub.10.1023/a:1020997118364
    27 sg:pub.10.1023/a:1021614115432
    28 sg:pub.10.1023/a:1026122726574
    29 sg:pub.10.1038/nature04525
    30 sg:pub.10.1038/nmeth0909-625
    31 sg:pub.10.1038/nsmb.2355
    32 sg:pub.10.1186/1471-2105-12-170
    33 https://doi.org/10.1002/(sici)1096-987x(19970115)18:1<139::aid-jcc13>3.0.co;2-h
    34 https://doi.org/10.1002/anie.201408598
    35 https://doi.org/10.1002/prot.20820
    36 https://doi.org/10.1006/jmbi.1994.0053
    37 https://doi.org/10.1006/jmbi.1995.0631
    38 https://doi.org/10.1006/jmbi.1997.1044
    39 https://doi.org/10.1006/jmbi.1997.1284
    40 https://doi.org/10.1016/0022-2836(85)90134-2
    41 https://doi.org/10.1016/0022-2836(91)90754-t
    42 https://doi.org/10.1016/0022-2836(91)90755-u
    43 https://doi.org/10.1016/j.str.2012.01.002
    44 https://doi.org/10.1016/j.str.2014.11.014
    45 https://doi.org/10.1016/s0022-2836(02)00241-3
    46 https://doi.org/10.1017/s0033583510000326
    47 https://doi.org/10.1017/s0033583598003436
    48 https://doi.org/10.1021/ja049786h
    49 https://doi.org/10.1021/ja061136l
    50 https://doi.org/10.1021/ja305091n
    51 https://doi.org/10.1093/bioinformatics/btl589
    52 https://doi.org/10.1093/nar/28.1.235
    53 https://doi.org/10.1093/nar/gkm957
    54 https://doi.org/10.1107/s1399004714026662
    55 schema:datePublished 2015-08
    56 schema:datePublishedReg 2015-08-01
    57 schema:description The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR.
    58 schema:genre research_article
    59 schema:inLanguage en
    60 schema:isAccessibleForFree false
    61 schema:isPartOf N1d579516d5724f46a8469e118d721b76
    62 N6935f3f0de1e4d6f81e3beef92fb47c5
    63 sg:journal.1101518
    64 schema:name Combined automated NOE assignment and structure calculation with CYANA
    65 schema:pagination 453-471
    66 schema:productId N210c9a8155364adf98823ab38640f9a7
    67 N7008f34d722f4cd5a4bd97a42f782cff
    68 Nbffc8e260ce44a378e1a53d8b5a7ba87
    69 Nd10cc992255c44bc86a0ba2e3c4884e2
    70 Nf7c882ec955f4809a0e5f84a592f450b
    71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042177174
    72 https://doi.org/10.1007/s10858-015-9924-9
    73 schema:sdDatePublished 2019-04-10T23:19
    74 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    75 schema:sdPublisher N113b16d54a984b899f6866848b0c9483
    76 schema:url http://link.springer.com/10.1007/s10858-015-9924-9
    77 sgo:license sg:explorer/license/
    78 sgo:sdDataset articles
    79 rdf:type schema:ScholarlyArticle
    80 N113b16d54a984b899f6866848b0c9483 schema:name Springer Nature - SN SciGraph project
    81 rdf:type schema:Organization
    82 N174b5c4459624e538f8cd36f3d507357 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    83 schema:name Models, Molecular
    84 rdf:type schema:DefinedTerm
    85 N1d579516d5724f46a8469e118d721b76 schema:volumeNumber 62
    86 rdf:type schema:PublicationVolume
    87 N210c9a8155364adf98823ab38640f9a7 schema:name nlm_unique_id
    88 schema:value 9110829
    89 rdf:type schema:PropertyValue
    90 N35b25c421fc94ec3bb2dccdecbff2882 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    91 schema:name Nuclear Magnetic Resonance, Biomolecular
    92 rdf:type schema:DefinedTerm
    93 N4513ed9235624a108bad846cfae3ddd4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    94 schema:name Software
    95 rdf:type schema:DefinedTerm
    96 N54dbae7321fe4073bb9e8432512f62f9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    97 schema:name Protein Conformation
    98 rdf:type schema:DefinedTerm
    99 N6935f3f0de1e4d6f81e3beef92fb47c5 schema:issueNumber 4
    100 rdf:type schema:PublicationIssue
    101 N7008f34d722f4cd5a4bd97a42f782cff schema:name doi
    102 schema:value 10.1007/s10858-015-9924-9
    103 rdf:type schema:PropertyValue
    104 N7c7c2593237e413d90c318e5066b60de rdf:first sg:person.01201353333.77
    105 rdf:rest Nf5b473148c8d45bc85ab0cca75e8902d
    106 N8be35a2421e34716ad048aaf14fb9624 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    107 schema:name Algorithms
    108 rdf:type schema:DefinedTerm
    109 N8eece340fecb4a609bf3861ba0038736 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    110 schema:name Proteins
    111 rdf:type schema:DefinedTerm
    112 Nbffc8e260ce44a378e1a53d8b5a7ba87 schema:name readcube_id
    113 schema:value c8e97e06e0eb6da3ec7271c31d7a6ee89a5b19cffd17df5e03280fa3fa48178a
    114 rdf:type schema:PropertyValue
    115 Nd10cc992255c44bc86a0ba2e3c4884e2 schema:name dimensions_id
    116 schema:value pub.1042177174
    117 rdf:type schema:PropertyValue
    118 Nf5b473148c8d45bc85ab0cca75e8902d rdf:first sg:person.01143034530.91
    119 rdf:rest rdf:nil
    120 Nf7c882ec955f4809a0e5f84a592f450b schema:name pubmed_id
    121 schema:value 25801209
    122 rdf:type schema:PropertyValue
    123 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    124 schema:name Biological Sciences
    125 rdf:type schema:DefinedTerm
    126 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    127 schema:name Biochemistry and Cell Biology
    128 rdf:type schema:DefinedTerm
    129 sg:grant.6119203 http://pending.schema.org/fundedItem sg:pub.10.1007/s10858-015-9924-9
    130 rdf:type schema:MonetaryGrant
    131 sg:journal.1101518 schema:issn 0925-2738
    132 1573-5001
    133 schema:name Journal of Biomolecular NMR
    134 rdf:type schema:Periodical
    135 sg:person.01143034530.91 schema:affiliation https://www.grid.ac/institutes/grid.7839.5
    136 schema:familyName Buchner
    137 schema:givenName Lena
    138 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01143034530.91
    139 rdf:type schema:Person
    140 sg:person.01201353333.77 schema:affiliation https://www.grid.ac/institutes/grid.265074.2
    141 schema:familyName Güntert
    142 schema:givenName Peter
    143 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201353333.77
    144 rdf:type schema:Person
    145 sg:pub.10.1007/bf00174613 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020274348
    146 https://doi.org/10.1007/bf00174613
    147 rdf:type schema:CreativeWork
    148 sg:pub.10.1007/bf00404272 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004332552
    149 https://doi.org/10.1007/bf00404272
    150 rdf:type schema:CreativeWork
    151 sg:pub.10.1007/bf00417486 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015332811
    152 https://doi.org/10.1007/bf00417486
    153 rdf:type schema:CreativeWork
    154 sg:pub.10.1007/bf02192850 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018314375
    155 https://doi.org/10.1007/bf02192850
    156 rdf:type schema:CreativeWork
    157 sg:pub.10.1007/s00249-008-0367-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1010435591
    158 https://doi.org/10.1007/s00249-008-0367-z
    159 rdf:type schema:CreativeWork
    160 sg:pub.10.1007/s10858-007-9175-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026134817
    161 https://doi.org/10.1007/s10858-007-9175-5
    162 rdf:type schema:CreativeWork
    163 sg:pub.10.1007/s10858-008-9295-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044926556
    164 https://doi.org/10.1007/s10858-008-9295-6
    165 rdf:type schema:CreativeWork
    166 sg:pub.10.1007/s10858-011-9502-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030537043
    167 https://doi.org/10.1007/s10858-011-9502-8
    168 rdf:type schema:CreativeWork
    169 sg:pub.10.1007/s10858-012-9615-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020000034
    170 https://doi.org/10.1007/s10858-012-9615-8
    171 rdf:type schema:CreativeWork
    172 sg:pub.10.1007/s10858-013-9708-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1015496408
    173 https://doi.org/10.1007/s10858-013-9708-z
    174 rdf:type schema:CreativeWork
    175 sg:pub.10.1007/s10858-013-9779-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1002638771
    176 https://doi.org/10.1007/s10858-013-9779-x
    177 rdf:type schema:CreativeWork
    178 sg:pub.10.1007/s10858-013-9780-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022005008
    179 https://doi.org/10.1007/s10858-013-9780-4
    180 rdf:type schema:CreativeWork
    181 sg:pub.10.1007/s10858-014-9832-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016735616
    182 https://doi.org/10.1007/s10858-014-9832-4
    183 rdf:type schema:CreativeWork
    184 sg:pub.10.1007/s10858-015-9921-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1012002218
    185 https://doi.org/10.1007/s10858-015-9921-z
    186 rdf:type schema:CreativeWork
    187 sg:pub.10.1023/a:1018383106236 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032527294
    188 https://doi.org/10.1023/a:1018383106236
    189 rdf:type schema:CreativeWork
    190 sg:pub.10.1023/a:1020279503261 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008990540
    191 https://doi.org/10.1023/a:1020279503261
    192 rdf:type schema:CreativeWork
    193 sg:pub.10.1023/a:1020997118364 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028389314
    194 https://doi.org/10.1023/a:1020997118364
    195 rdf:type schema:CreativeWork
    196 sg:pub.10.1023/a:1021614115432 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038114673
    197 https://doi.org/10.1023/a:1021614115432
    198 rdf:type schema:CreativeWork
    199 sg:pub.10.1023/a:1026122726574 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004234144
    200 https://doi.org/10.1023/a:1026122726574
    201 rdf:type schema:CreativeWork
    202 sg:pub.10.1038/nature04525 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019716667
    203 https://doi.org/10.1038/nature04525
    204 rdf:type schema:CreativeWork
    205 sg:pub.10.1038/nmeth0909-625 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032293100
    206 https://doi.org/10.1038/nmeth0909-625
    207 rdf:type schema:CreativeWork
    208 sg:pub.10.1038/nsmb.2355 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010043458
    209 https://doi.org/10.1038/nsmb.2355
    210 rdf:type schema:CreativeWork
    211 sg:pub.10.1186/1471-2105-12-170 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010022232
    212 https://doi.org/10.1186/1471-2105-12-170
    213 rdf:type schema:CreativeWork
    214 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
    215 rdf:type schema:CreativeWork
    216 https://doi.org/10.1002/anie.201408598 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023290329
    217 rdf:type schema:CreativeWork
    218 https://doi.org/10.1002/prot.20820 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051962266
    219 rdf:type schema:CreativeWork
    220 https://doi.org/10.1006/jmbi.1994.0053 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022908229
    221 rdf:type schema:CreativeWork
    222 https://doi.org/10.1006/jmbi.1995.0631 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038786017
    223 rdf:type schema:CreativeWork
    224 https://doi.org/10.1006/jmbi.1997.1044 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023394964
    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/10.1016/0022-2836(85)90134-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035083567
    229 rdf:type schema:CreativeWork
    230 https://doi.org/10.1016/0022-2836(91)90754-t schema:sameAs https://app.dimensions.ai/details/publication/pub.1036024947
    231 rdf:type schema:CreativeWork
    232 https://doi.org/10.1016/0022-2836(91)90755-u schema:sameAs https://app.dimensions.ai/details/publication/pub.1005616750
    233 rdf:type schema:CreativeWork
    234 https://doi.org/10.1016/j.str.2012.01.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004887871
    235 rdf:type schema:CreativeWork
    236 https://doi.org/10.1016/j.str.2014.11.014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039036820
    237 rdf:type schema:CreativeWork
    238 https://doi.org/10.1016/s0022-2836(02)00241-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011905922
    239 rdf:type schema:CreativeWork
    240 https://doi.org/10.1017/s0033583510000326 schema:sameAs https://app.dimensions.ai/details/publication/pub.1054060929
    241 rdf:type schema:CreativeWork
    242 https://doi.org/10.1017/s0033583598003436 schema:sameAs https://app.dimensions.ai/details/publication/pub.1054077673
    243 rdf:type schema:CreativeWork
    244 https://doi.org/10.1021/ja049786h schema:sameAs https://app.dimensions.ai/details/publication/pub.1055838207
    245 rdf:type schema:CreativeWork
    246 https://doi.org/10.1021/ja061136l schema:sameAs https://app.dimensions.ai/details/publication/pub.1002363078
    247 rdf:type schema:CreativeWork
    248 https://doi.org/10.1021/ja305091n schema:sameAs https://app.dimensions.ai/details/publication/pub.1037057740
    249 rdf:type schema:CreativeWork
    250 https://doi.org/10.1093/bioinformatics/btl589 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012374959
    251 rdf:type schema:CreativeWork
    252 https://doi.org/10.1093/nar/28.1.235 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035055456
    253 rdf:type schema:CreativeWork
    254 https://doi.org/10.1093/nar/gkm957 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025566031
    255 rdf:type schema:CreativeWork
    256 https://doi.org/10.1107/s1399004714026662 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014436414
    257 rdf:type schema:CreativeWork
    258 https://www.grid.ac/institutes/grid.265074.2 schema:alternateName Tokyo Metropolitan University
    259 schema:name Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
    260 Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
    261 Laboratory of Physical Chemistry, ETH Zürich, Zurich, Switzerland
    262 rdf:type schema:Organization
    263 https://www.grid.ac/institutes/grid.7839.5 schema:alternateName Goethe University Frankfurt
    264 schema:name Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
    265 rdf:type schema:Organization
     




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


    ...