1,000 structures and more from the MCSG View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-12

AUTHORS

David Lee, Tjaart AP de Beer, Roman A Laskowski, Janet M Thornton, Christine A Orengo

ABSTRACT

BACKGROUND: The Midwest Center for Structural Genomics (MCSG) is one of the large-scale centres of the Protein Structure Initiative (PSI). During the first two phases of the PSI the MCSG has solved over a thousand protein structures. A criticism of structural genomics is that target selection strategies mean that some structures are solved without having a known function and thus are of little biomedical significance. Structures of unknown function have stimulated the development of methods for function prediction from structure. RESULTS: We show that the MCSG has met the stated goals of the PSI and use online resources and readily available function prediction methods to provide functional annotations for more than 90% of the MCSG structures. The structure-to-function prediction method ProFunc provides likely functions for many of the MCSG structures that cannot be annotated by sequence-based methods. CONCLUSIONS: Although the focus of the PSI was structural coverage, many of the structures solved by the MCSG can also be associated with functional classes and biological roles of possible biomedical value. More... »

PAGES

2

References to SciGraph publications

  • 2009-03. The Protein Model Portal in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS
  • 2000-05. Gene Ontology: tool for the unification of biology in NATURE GENETICS
  • 2009-04. Structural genomics is the largest contributor of novel structural leverage in JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS
  • 2007-08. Novel leverage of structural genomics in NATURE BIOTECHNOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1472-6807-11-2

    DOI

    http://dx.doi.org/10.1186/1472-6807-11-2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1011736077

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21219649


    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": "Base Sequence", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Computational Biology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Databases, Protein", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mutation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Online Systems", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Conformation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Structure, Quaternary", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Protein Structure, Secondary", 
            "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": "Proteomics", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "University College London", 
              "id": "https://www.grid.ac/institutes/grid.83440.3b", 
              "name": [
                "Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Lee", 
            "givenName": "David", 
            "id": "sg:person.01026543167.44", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01026543167.44"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "European Bioinformatics Institute", 
              "id": "https://www.grid.ac/institutes/grid.225360.0", 
              "name": [
                "European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "de Beer", 
            "givenName": "Tjaart AP", 
            "id": "sg:person.010722720734.13", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010722720734.13"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "European Bioinformatics Institute", 
              "id": "https://www.grid.ac/institutes/grid.225360.0", 
              "name": [
                "European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Laskowski", 
            "givenName": "Roman A", 
            "id": "sg:person.0755644042.97", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755644042.97"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "European Bioinformatics Institute", 
              "id": "https://www.grid.ac/institutes/grid.225360.0", 
              "name": [
                "European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Thornton", 
            "givenName": "Janet M", 
            "id": "sg:person.01077347144.47", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01077347144.47"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University College London", 
              "id": "https://www.grid.ac/institutes/grid.83440.3b", 
              "name": [
                "Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Orengo", 
            "givenName": "Christine A", 
            "id": "sg:person.01136244107.52", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136244107.52"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1093/nar/gkn808", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002099926"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt0807-849", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002363423", 
              "https://doi.org/10.1038/nbt0807-849"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bib/3.3.265", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002415830"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gki414", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005170891"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkl1043", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005543336"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.0010031", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006324169"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.0010031", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006324169"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10969-008-9048-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006341800", 
              "https://doi.org/10.1007/s10969-008-9048-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkp846", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006602999"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/14.10.846", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007408967"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.str.2009.03.015", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008767336"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1574-6968.2009.01777.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009838623"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.0030232", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010637133"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkp896", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013384337"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkp987", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013810478"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btl158", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014668137"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btg226", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015072842"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkp916", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015188926"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkp916", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015188926"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/28.1.304", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015734752"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/protein/11.10.855", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015934605"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/prot.20298", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016124748"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10969-008-9055-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016294894", 
              "https://doi.org/10.1007/s10969-008-9055-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkp985", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016317136"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1574-6968.1997.tb12776.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018680741"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1574-6968.1997.tb12776.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018680741"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pcbi.1000485", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019010274"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1121018", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019170932"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1042/bj20041480", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022535377"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1042/bj20041480", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022535377"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkl959", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027465591"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.0611678104", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027555433"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/dnares/dsm018", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1029046144"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0022-2836(05)80134-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030477247"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btg224", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030521598"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.772403", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030905286"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkn860", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031182315"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.str.2007.11.004", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031746182"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btn504", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032445030"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jmb.2005.03.037", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032995227"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jmb.2004.12.032", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033002999"
            ], 
            "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/10.1073/pnas.85.8.2444", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035928070"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkj494", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038367016"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0076-6879(96)66038-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043405451"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkh028", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043666429"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/75556", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044135237", 
              "https://doi.org/10.1038/75556"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/75556", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044135237", 
              "https://doi.org/10.1038/75556"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkn790", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044731397"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/25.17.3389", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047265454"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jmb.2007.01.063", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1047650557"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jmb.2005.05.067", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048589454"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1086/506389", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1058785225"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1174671", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062460208"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1174671", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062460208"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2011-12", 
        "datePublishedReg": "2011-12-01", 
        "description": "BACKGROUND: The Midwest Center for Structural Genomics (MCSG) is one of the large-scale centres of the Protein Structure Initiative (PSI). During the first two phases of the PSI the MCSG has solved over a thousand protein structures. A criticism of structural genomics is that target selection strategies mean that some structures are solved without having a known function and thus are of little biomedical significance. Structures of unknown function have stimulated the development of methods for function prediction from structure.\nRESULTS: We show that the MCSG has met the stated goals of the PSI and use online resources and readily available function prediction methods to provide functional annotations for more than 90% of the MCSG structures. The structure-to-function prediction method ProFunc provides likely functions for many of the MCSG structures that cannot be annotated by sequence-based methods.\nCONCLUSIONS: Although the focus of the PSI was structural coverage, many of the structures solved by the MCSG can also be associated with functional classes and biological roles of possible biomedical value.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1186/1472-6807-11-2", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2699232", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1028437", 
            "issn": [
              "2314-4343", 
              "1472-6807"
            ], 
            "name": "BMC Structural Biology", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "11"
          }
        ], 
        "name": "1,000 structures and more from the MCSG", 
        "pagination": "2", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "37ea862e022a48cf4a446b02bc106d38ca8ce91cb8a49230b07a25a764e17b17"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "21219649"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "101088689"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/1472-6807-11-2"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1011736077"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/1472-6807-11-2", 
          "https://app.dimensions.ai/details/publication/pub.1011736077"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T18:20", 
        "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_8675_00000511.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1186%2F1472-6807-11-2"
      }
    ]
     

    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.10.1186/1472-6807-11-2'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1472-6807-11-2'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1472-6807-11-2'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1472-6807-11-2'


     

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

    309 TRIPLES      21 PREDICATES      92 URIs      35 LITERALS      23 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/1472-6807-11-2 schema:about N036dbee5f1834b10bddb994236f9975f
    2 N265944b4ec594be68dbea233ef058c9d
    3 N27413edaaa3d485d9d969bb3a6dc2c85
    4 N2f06f0fb535a4ba1a7982f147757664c
    5 N332c9e7825014551a0a5535744cc37df
    6 N33970173719c44b9bfba83060948ec8f
    7 N3a9f923499794cc79ca347c110037a66
    8 N5ecf3f73cdf04b79b965604fb9dc2fb3
    9 N661cd23a06fd43ffba1219d3413498d7
    10 N70c3a94df6dd42acb33f5fae0b4cca85
    11 Na72f48450fb84996917cd104852ebe69
    12 Na9f4982794f649af853750f873fc9865
    13 Nbdb22ec899314247a40ee0efd7745ecf
    14 Ndf4df2b7e8b740cfb0c10e58bb82f902
    15 anzsrc-for:06
    16 anzsrc-for:0601
    17 schema:author N52e7f5216b904fffbe0db0f080ecff05
    18 schema:citation sg:pub.10.1007/s10969-008-9048-5
    19 sg:pub.10.1007/s10969-008-9055-6
    20 sg:pub.10.1038/75556
    21 sg:pub.10.1038/nbt0807-849
    22 https://doi.org/10.1002/prot.20298
    23 https://doi.org/10.1016/j.jmb.2004.12.032
    24 https://doi.org/10.1016/j.jmb.2005.03.037
    25 https://doi.org/10.1016/j.jmb.2005.05.067
    26 https://doi.org/10.1016/j.jmb.2007.01.063
    27 https://doi.org/10.1016/j.str.2007.11.004
    28 https://doi.org/10.1016/j.str.2009.03.015
    29 https://doi.org/10.1016/s0022-2836(05)80134-2
    30 https://doi.org/10.1016/s0076-6879(96)66038-8
    31 https://doi.org/10.1042/bj20041480
    32 https://doi.org/10.1073/pnas.0611678104
    33 https://doi.org/10.1073/pnas.85.8.2444
    34 https://doi.org/10.1086/506389
    35 https://doi.org/10.1093/bib/3.3.265
    36 https://doi.org/10.1093/bioinformatics/14.10.846
    37 https://doi.org/10.1093/bioinformatics/btg224
    38 https://doi.org/10.1093/bioinformatics/btg226
    39 https://doi.org/10.1093/bioinformatics/btl158
    40 https://doi.org/10.1093/bioinformatics/btn504
    41 https://doi.org/10.1093/dnares/dsm018
    42 https://doi.org/10.1093/nar/25.17.3389
    43 https://doi.org/10.1093/nar/28.1.235
    44 https://doi.org/10.1093/nar/28.1.304
    45 https://doi.org/10.1093/nar/gkh028
    46 https://doi.org/10.1093/nar/gki414
    47 https://doi.org/10.1093/nar/gkj494
    48 https://doi.org/10.1093/nar/gkl1043
    49 https://doi.org/10.1093/nar/gkl959
    50 https://doi.org/10.1093/nar/gkn790
    51 https://doi.org/10.1093/nar/gkn808
    52 https://doi.org/10.1093/nar/gkn860
    53 https://doi.org/10.1093/nar/gkp846
    54 https://doi.org/10.1093/nar/gkp896
    55 https://doi.org/10.1093/nar/gkp916
    56 https://doi.org/10.1093/nar/gkp985
    57 https://doi.org/10.1093/nar/gkp987
    58 https://doi.org/10.1093/protein/11.10.855
    59 https://doi.org/10.1101/gr.772403
    60 https://doi.org/10.1111/j.1574-6968.1997.tb12776.x
    61 https://doi.org/10.1111/j.1574-6968.2009.01777.x
    62 https://doi.org/10.1126/science.1121018
    63 https://doi.org/10.1126/science.1174671
    64 https://doi.org/10.1371/journal.pcbi.0010031
    65 https://doi.org/10.1371/journal.pcbi.0030232
    66 https://doi.org/10.1371/journal.pcbi.1000485
    67 schema:datePublished 2011-12
    68 schema:datePublishedReg 2011-12-01
    69 schema:description BACKGROUND: The Midwest Center for Structural Genomics (MCSG) is one of the large-scale centres of the Protein Structure Initiative (PSI). During the first two phases of the PSI the MCSG has solved over a thousand protein structures. A criticism of structural genomics is that target selection strategies mean that some structures are solved without having a known function and thus are of little biomedical significance. Structures of unknown function have stimulated the development of methods for function prediction from structure. RESULTS: We show that the MCSG has met the stated goals of the PSI and use online resources and readily available function prediction methods to provide functional annotations for more than 90% of the MCSG structures. The structure-to-function prediction method ProFunc provides likely functions for many of the MCSG structures that cannot be annotated by sequence-based methods. CONCLUSIONS: Although the focus of the PSI was structural coverage, many of the structures solved by the MCSG can also be associated with functional classes and biological roles of possible biomedical value.
    70 schema:genre research_article
    71 schema:inLanguage en
    72 schema:isAccessibleForFree true
    73 schema:isPartOf N02dccbb9096f45c18b18d67e06e36c33
    74 N6337a7b0719a420a895a14d99b1ed69c
    75 sg:journal.1028437
    76 schema:name 1,000 structures and more from the MCSG
    77 schema:pagination 2
    78 schema:productId N6a74ae0eb1c74ceb93ff2ef4e62af4ad
    79 N85a1ba992e174ebabc481f8dcdadbea5
    80 Na31b4388fd354c6ba9dd3e932b009fad
    81 Ned37905db64141ed83ebdaab66a1d32f
    82 Nf53fdac04b4745a0a3d7029ab9eae46a
    83 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011736077
    84 https://doi.org/10.1186/1472-6807-11-2
    85 schema:sdDatePublished 2019-04-10T18:20
    86 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    87 schema:sdPublisher Nffe658501ad84ddc80b5d31fd7c40951
    88 schema:url http://link.springer.com/10.1186%2F1472-6807-11-2
    89 sgo:license sg:explorer/license/
    90 sgo:sdDataset articles
    91 rdf:type schema:ScholarlyArticle
    92 N02dccbb9096f45c18b18d67e06e36c33 schema:volumeNumber 11
    93 rdf:type schema:PublicationVolume
    94 N036dbee5f1834b10bddb994236f9975f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    95 schema:name Protein Structure, Tertiary
    96 rdf:type schema:DefinedTerm
    97 N265944b4ec594be68dbea233ef058c9d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    98 schema:name Databases, Protein
    99 rdf:type schema:DefinedTerm
    100 N27413edaaa3d485d9d969bb3a6dc2c85 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    101 schema:name Proteomics
    102 rdf:type schema:DefinedTerm
    103 N2f06f0fb535a4ba1a7982f147757664c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    104 schema:name Genomics
    105 rdf:type schema:DefinedTerm
    106 N332c9e7825014551a0a5535744cc37df schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    107 schema:name Protein Conformation
    108 rdf:type schema:DefinedTerm
    109 N33970173719c44b9bfba83060948ec8f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    110 schema:name Genome
    111 rdf:type schema:DefinedTerm
    112 N3a9f923499794cc79ca347c110037a66 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    113 schema:name Mutation
    114 rdf:type schema:DefinedTerm
    115 N52e7f5216b904fffbe0db0f080ecff05 rdf:first sg:person.01026543167.44
    116 rdf:rest Nce6824a605874c07a14a28bf30fbf16b
    117 N5ecf3f73cdf04b79b965604fb9dc2fb3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    118 schema:name Protein Structure, Quaternary
    119 rdf:type schema:DefinedTerm
    120 N6337a7b0719a420a895a14d99b1ed69c schema:issueNumber 1
    121 rdf:type schema:PublicationIssue
    122 N661cd23a06fd43ffba1219d3413498d7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    123 schema:name Base Sequence
    124 rdf:type schema:DefinedTerm
    125 N68de92e8d4da49b3af77ab604784378a rdf:first sg:person.0755644042.97
    126 rdf:rest Nff65052efa7a4ff0b41e9ffbd76a5c0b
    127 N6a74ae0eb1c74ceb93ff2ef4e62af4ad schema:name nlm_unique_id
    128 schema:value 101088689
    129 rdf:type schema:PropertyValue
    130 N70c3a94df6dd42acb33f5fae0b4cca85 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    131 schema:name Computational Biology
    132 rdf:type schema:DefinedTerm
    133 N85a1ba992e174ebabc481f8dcdadbea5 schema:name readcube_id
    134 schema:value 37ea862e022a48cf4a446b02bc106d38ca8ce91cb8a49230b07a25a764e17b17
    135 rdf:type schema:PropertyValue
    136 N97aa7deb81d34a66a24eb679ccd56756 rdf:first sg:person.01136244107.52
    137 rdf:rest rdf:nil
    138 Na31b4388fd354c6ba9dd3e932b009fad schema:name dimensions_id
    139 schema:value pub.1011736077
    140 rdf:type schema:PropertyValue
    141 Na72f48450fb84996917cd104852ebe69 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    142 schema:name Proteins
    143 rdf:type schema:DefinedTerm
    144 Na9f4982794f649af853750f873fc9865 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    145 schema:name Amino Acid Sequence
    146 rdf:type schema:DefinedTerm
    147 Nbdb22ec899314247a40ee0efd7745ecf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    148 schema:name Online Systems
    149 rdf:type schema:DefinedTerm
    150 Nce6824a605874c07a14a28bf30fbf16b rdf:first sg:person.010722720734.13
    151 rdf:rest N68de92e8d4da49b3af77ab604784378a
    152 Ndf4df2b7e8b740cfb0c10e58bb82f902 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    153 schema:name Protein Structure, Secondary
    154 rdf:type schema:DefinedTerm
    155 Ned37905db64141ed83ebdaab66a1d32f schema:name doi
    156 schema:value 10.1186/1472-6807-11-2
    157 rdf:type schema:PropertyValue
    158 Nf53fdac04b4745a0a3d7029ab9eae46a schema:name pubmed_id
    159 schema:value 21219649
    160 rdf:type schema:PropertyValue
    161 Nff65052efa7a4ff0b41e9ffbd76a5c0b rdf:first sg:person.01077347144.47
    162 rdf:rest N97aa7deb81d34a66a24eb679ccd56756
    163 Nffe658501ad84ddc80b5d31fd7c40951 schema:name Springer Nature - SN SciGraph project
    164 rdf:type schema:Organization
    165 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    166 schema:name Biological Sciences
    167 rdf:type schema:DefinedTerm
    168 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    169 schema:name Biochemistry and Cell Biology
    170 rdf:type schema:DefinedTerm
    171 sg:grant.2699232 http://pending.schema.org/fundedItem sg:pub.10.1186/1472-6807-11-2
    172 rdf:type schema:MonetaryGrant
    173 sg:journal.1028437 schema:issn 1472-6807
    174 2314-4343
    175 schema:name BMC Structural Biology
    176 rdf:type schema:Periodical
    177 sg:person.01026543167.44 schema:affiliation https://www.grid.ac/institutes/grid.83440.3b
    178 schema:familyName Lee
    179 schema:givenName David
    180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01026543167.44
    181 rdf:type schema:Person
    182 sg:person.010722720734.13 schema:affiliation https://www.grid.ac/institutes/grid.225360.0
    183 schema:familyName de Beer
    184 schema:givenName Tjaart AP
    185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010722720734.13
    186 rdf:type schema:Person
    187 sg:person.01077347144.47 schema:affiliation https://www.grid.ac/institutes/grid.225360.0
    188 schema:familyName Thornton
    189 schema:givenName Janet M
    190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01077347144.47
    191 rdf:type schema:Person
    192 sg:person.01136244107.52 schema:affiliation https://www.grid.ac/institutes/grid.83440.3b
    193 schema:familyName Orengo
    194 schema:givenName Christine A
    195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136244107.52
    196 rdf:type schema:Person
    197 sg:person.0755644042.97 schema:affiliation https://www.grid.ac/institutes/grid.225360.0
    198 schema:familyName Laskowski
    199 schema:givenName Roman A
    200 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755644042.97
    201 rdf:type schema:Person
    202 sg:pub.10.1007/s10969-008-9048-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006341800
    203 https://doi.org/10.1007/s10969-008-9048-5
    204 rdf:type schema:CreativeWork
    205 sg:pub.10.1007/s10969-008-9055-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016294894
    206 https://doi.org/10.1007/s10969-008-9055-6
    207 rdf:type schema:CreativeWork
    208 sg:pub.10.1038/75556 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044135237
    209 https://doi.org/10.1038/75556
    210 rdf:type schema:CreativeWork
    211 sg:pub.10.1038/nbt0807-849 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002363423
    212 https://doi.org/10.1038/nbt0807-849
    213 rdf:type schema:CreativeWork
    214 https://doi.org/10.1002/prot.20298 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016124748
    215 rdf:type schema:CreativeWork
    216 https://doi.org/10.1016/j.jmb.2004.12.032 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033002999
    217 rdf:type schema:CreativeWork
    218 https://doi.org/10.1016/j.jmb.2005.03.037 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032995227
    219 rdf:type schema:CreativeWork
    220 https://doi.org/10.1016/j.jmb.2005.05.067 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048589454
    221 rdf:type schema:CreativeWork
    222 https://doi.org/10.1016/j.jmb.2007.01.063 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047650557
    223 rdf:type schema:CreativeWork
    224 https://doi.org/10.1016/j.str.2007.11.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031746182
    225 rdf:type schema:CreativeWork
    226 https://doi.org/10.1016/j.str.2009.03.015 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008767336
    227 rdf:type schema:CreativeWork
    228 https://doi.org/10.1016/s0022-2836(05)80134-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030477247
    229 rdf:type schema:CreativeWork
    230 https://doi.org/10.1016/s0076-6879(96)66038-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043405451
    231 rdf:type schema:CreativeWork
    232 https://doi.org/10.1042/bj20041480 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022535377
    233 rdf:type schema:CreativeWork
    234 https://doi.org/10.1073/pnas.0611678104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027555433
    235 rdf:type schema:CreativeWork
    236 https://doi.org/10.1073/pnas.85.8.2444 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035928070
    237 rdf:type schema:CreativeWork
    238 https://doi.org/10.1086/506389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058785225
    239 rdf:type schema:CreativeWork
    240 https://doi.org/10.1093/bib/3.3.265 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002415830
    241 rdf:type schema:CreativeWork
    242 https://doi.org/10.1093/bioinformatics/14.10.846 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007408967
    243 rdf:type schema:CreativeWork
    244 https://doi.org/10.1093/bioinformatics/btg224 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030521598
    245 rdf:type schema:CreativeWork
    246 https://doi.org/10.1093/bioinformatics/btg226 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015072842
    247 rdf:type schema:CreativeWork
    248 https://doi.org/10.1093/bioinformatics/btl158 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014668137
    249 rdf:type schema:CreativeWork
    250 https://doi.org/10.1093/bioinformatics/btn504 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032445030
    251 rdf:type schema:CreativeWork
    252 https://doi.org/10.1093/dnares/dsm018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029046144
    253 rdf:type schema:CreativeWork
    254 https://doi.org/10.1093/nar/25.17.3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047265454
    255 rdf:type schema:CreativeWork
    256 https://doi.org/10.1093/nar/28.1.235 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035055456
    257 rdf:type schema:CreativeWork
    258 https://doi.org/10.1093/nar/28.1.304 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015734752
    259 rdf:type schema:CreativeWork
    260 https://doi.org/10.1093/nar/gkh028 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043666429
    261 rdf:type schema:CreativeWork
    262 https://doi.org/10.1093/nar/gki414 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005170891
    263 rdf:type schema:CreativeWork
    264 https://doi.org/10.1093/nar/gkj494 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038367016
    265 rdf:type schema:CreativeWork
    266 https://doi.org/10.1093/nar/gkl1043 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005543336
    267 rdf:type schema:CreativeWork
    268 https://doi.org/10.1093/nar/gkl959 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027465591
    269 rdf:type schema:CreativeWork
    270 https://doi.org/10.1093/nar/gkn790 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044731397
    271 rdf:type schema:CreativeWork
    272 https://doi.org/10.1093/nar/gkn808 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002099926
    273 rdf:type schema:CreativeWork
    274 https://doi.org/10.1093/nar/gkn860 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031182315
    275 rdf:type schema:CreativeWork
    276 https://doi.org/10.1093/nar/gkp846 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006602999
    277 rdf:type schema:CreativeWork
    278 https://doi.org/10.1093/nar/gkp896 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013384337
    279 rdf:type schema:CreativeWork
    280 https://doi.org/10.1093/nar/gkp916 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015188926
    281 rdf:type schema:CreativeWork
    282 https://doi.org/10.1093/nar/gkp985 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016317136
    283 rdf:type schema:CreativeWork
    284 https://doi.org/10.1093/nar/gkp987 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013810478
    285 rdf:type schema:CreativeWork
    286 https://doi.org/10.1093/protein/11.10.855 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015934605
    287 rdf:type schema:CreativeWork
    288 https://doi.org/10.1101/gr.772403 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030905286
    289 rdf:type schema:CreativeWork
    290 https://doi.org/10.1111/j.1574-6968.1997.tb12776.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1018680741
    291 rdf:type schema:CreativeWork
    292 https://doi.org/10.1111/j.1574-6968.2009.01777.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1009838623
    293 rdf:type schema:CreativeWork
    294 https://doi.org/10.1126/science.1121018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019170932
    295 rdf:type schema:CreativeWork
    296 https://doi.org/10.1126/science.1174671 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062460208
    297 rdf:type schema:CreativeWork
    298 https://doi.org/10.1371/journal.pcbi.0010031 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006324169
    299 rdf:type schema:CreativeWork
    300 https://doi.org/10.1371/journal.pcbi.0030232 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010637133
    301 rdf:type schema:CreativeWork
    302 https://doi.org/10.1371/journal.pcbi.1000485 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019010274
    303 rdf:type schema:CreativeWork
    304 https://www.grid.ac/institutes/grid.225360.0 schema:alternateName European Bioinformatics Institute
    305 schema:name European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
    306 rdf:type schema:Organization
    307 https://www.grid.ac/institutes/grid.83440.3b schema:alternateName University College London
    308 schema:name Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, UK
    309 rdf:type schema:Organization
     




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


    ...