Partition function and base pairing probabilities of RNA heterodimers View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-01

AUTHORS

Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F Stadler, Ivo L Hofacker

ABSTRACT

BACKGROUND: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. METHODS: The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. RESULTS: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures. More... »

PAGES

3

References to SciGraph publications

  • 2005-04. Evolutionary patterns of non-coding RNAs in THEORY IN BIOSCIENCES
  • 2004-05. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs in NATURE REVIEWS GENETICS
  • 2004-04. RNA regulation: a new genetics? in NATURE REVIEWS GENETICS
  • 1994-02. Fast folding and comparison of RNA secondary structures in MONATSHEFTE FÜR CHEMIE - CHEMICAL MONTHLY
  • 2004-12. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics in BMC BIOINFORMATICS
  • 1984. RNA secondary structures and their prediction in BULLETIN OF MATHEMATICAL BIOLOGY
  • 2004-09. The functions of animal microRNAs in NATURE
  • 2005-11. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome in NATURE BIOTECHNOLOGY
  • 1984-07. RNA secondary structures and their prediction in BULLETIN OF MATHEMATICAL BIOLOGY
  • 1998-03. A coat for all sequences in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1748-7188-1-3

    DOI

    http://dx.doi.org/10.1186/1748-7188-1-3

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1049447594

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/16722605


    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"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "University of Vienna", 
              "id": "https://www.grid.ac/institutes/grid.10420.37", 
              "name": [
                "Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, Vienna, Austria"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Bernhart", 
            "givenName": "Stephan H", 
            "id": "sg:person.0753447607.17", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0753447607.17"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Vienna", 
              "id": "https://www.grid.ac/institutes/grid.10420.37", 
              "name": [
                "Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, Vienna, Austria"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tafer", 
            "givenName": "Hakim", 
            "id": "sg:person.0755677032.58", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755677032.58"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Vienna", 
              "id": "https://www.grid.ac/institutes/grid.10420.37", 
              "name": [
                "Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, Vienna, Austria"
              ], 
              "type": "Organization"
            }, 
            "familyName": "M\u00fcckstein", 
            "givenName": "Ulrike", 
            "id": "sg:person.0612150527.13", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0612150527.13"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Vienna", 
              "id": "https://www.grid.ac/institutes/grid.10420.37", 
              "name": [
                "Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16\u201318, D-04170, Leipzig, Germany", 
                "Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, Vienna, Austria"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Flamm", 
            "givenName": "Christoph", 
            "id": "sg:person.01110764033.35", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110764033.35"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Santa Fe Institute", 
              "id": "https://www.grid.ac/institutes/grid.209665.e", 
              "name": [
                "Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16\u201318, D-04170, Leipzig, Germany", 
                "Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, Vienna, Austria", 
                "The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, New Mexico"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Stadler", 
            "givenName": "Peter F", 
            "id": "sg:person.0664150133.70", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0664150133.70"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "University of Vienna", 
              "id": "https://www.grid.ac/institutes/grid.10420.37", 
              "name": [
                "Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, Vienna, Austria"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hofacker", 
            "givenName": "Ivo L", 
            "id": "sg:person.01222322364.52", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01222322364.52"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1101/gad.862301", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000961502"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1046/j.1432-1033.2002.02970.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1001442923"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/9.1.133", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004222010"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/29.5.1034", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005082622"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.tibs.2003.08.005", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005576380"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.tibs.2003.08.005", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005576380"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkg938", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007345576"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0092-8674(04)00127-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008587641"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.95.4.1460", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009187647"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkg595", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013618001"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg1321", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013684976", 
              "https://doi.org/10.1038/nrg1321"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg1321", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013684976", 
              "https://doi.org/10.1038/nrg1321"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkh841", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016061119"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/cbic.200400219", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016880030"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkg599", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017511013"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.172391199", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018259290"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.gene.2004.11.043", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018808147"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg1328", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019747892", 
              "https://doi.org/10.1038/nrg1328"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg1328", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019747892", 
              "https://doi.org/10.1038/nrg1328"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/s0960-9822(01)00401-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021943538"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.tibs.2004.07.001", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022439096"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1016/j.thbio.2005.01.002", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022966750", 
              "https://doi.org/10.1016/j.thbio.2005.01.002"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1529/biophysj.103.020743", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023790799"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jmb.2004.10.082", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023879738"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gad.1184404", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024436325"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkg438", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025084080"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/(sici)1097-0282(199902)49:2<145::aid-bip4>3.0.co;2-g", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025101661"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.0401799101", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026962739"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-5-104", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028464672", 
              "https://doi.org/10.1186/1471-2105-5-104"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt1144", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028917438", 
              "https://doi.org/10.1038/nbt1144"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt1144", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028917438", 
              "https://doi.org/10.1038/nbt1144"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt1144", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028917438", 
              "https://doi.org/10.1038/nbt1144"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1006/jmbi.1998.2436", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030245324"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1146/annurev.genet.34.1.499", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031435901"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.jmb.2005.03.011", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032159466"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/bip.360290621", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032289021"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf00818163", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032495505", 
              "https://doi.org/10.1007/bf00818163"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1261/rna.5248604", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034010998"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/bies.10332", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034594169"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1006/jmbi.1999.2700", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034604829"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/j.pbi.2004.11.008", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035292807"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.112063799", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040956624"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1103388", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042123507"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02871", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043341870", 
              "https://doi.org/10.1038/nature02871"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature02871", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043341870", 
              "https://doi.org/10.1038/nature02871"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nsb0398-174", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045619143", 
              "https://doi.org/10.1038/nsb0398-174"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gnh076", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046119255"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.1108625", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046921907"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/bti1113", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049107232"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.2094104", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050487471"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1002/jcc.10296", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051970143"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf02459506", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052391942", 
              "https://doi.org/10.1007/bf02459506"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/bf02459506", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052391942", 
              "https://doi.org/10.1007/bf02459506"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/gkh706", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053499486"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1016/s0092-8240(84)80062-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1054614704", 
              "https://doi.org/10.1016/s0092-8240(84)80062-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.2468181", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062538914"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1137/0135006", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062839734"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://app.dimensions.ai/details/publication/pub.1083073479", 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2006-01", 
        "datePublishedReg": "2006-01-01", 
        "description": "BACKGROUND: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms.\nMETHODS: The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs.\nRESULTS: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1186/1748-7188-1-3", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1036449", 
            "issn": [
              "1748-7188"
            ], 
            "name": "Algorithms for Molecular Biology", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "1"
          }
        ], 
        "name": "Partition function and base pairing probabilities of RNA heterodimers", 
        "pagination": "3", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "eb8ec5170e7f5415cded7983c63f64c00529cf01318e42ea3c75d3b9f41e6ddd"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "16722605"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "101265088"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/1748-7188-1-3"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1049447594"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/1748-7188-1-3", 
          "https://app.dimensions.ai/details/publication/pub.1049447594"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T13:18", 
        "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_8659_00000516.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1186%2F1748-7188-1-3"
      }
    ]
     

    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.10.1186/1748-7188-1-3'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1748-7188-1-3'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1748-7188-1-3'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1748-7188-1-3'


     

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

    271 TRIPLES      21 PREDICATES      80 URIs      21 LITERALS      9 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/1748-7188-1-3 schema:about anzsrc-for:06
    2 anzsrc-for:0601
    3 schema:author N4f8115f2d76745b4990e296629f68162
    4 schema:citation sg:pub.10.1007/bf00818163
    5 sg:pub.10.1007/bf02459506
    6 sg:pub.10.1016/j.thbio.2005.01.002
    7 sg:pub.10.1016/s0092-8240(84)80062-2
    8 sg:pub.10.1038/nature02871
    9 sg:pub.10.1038/nbt1144
    10 sg:pub.10.1038/nrg1321
    11 sg:pub.10.1038/nrg1328
    12 sg:pub.10.1038/nsb0398-174
    13 sg:pub.10.1186/1471-2105-5-104
    14 https://app.dimensions.ai/details/publication/pub.1083073479
    15 https://doi.org/10.1002/(sici)1097-0282(199902)49:2<145::aid-bip4>3.0.co;2-g
    16 https://doi.org/10.1002/bies.10332
    17 https://doi.org/10.1002/bip.360290621
    18 https://doi.org/10.1002/cbic.200400219
    19 https://doi.org/10.1002/jcc.10296
    20 https://doi.org/10.1006/jmbi.1998.2436
    21 https://doi.org/10.1006/jmbi.1999.2700
    22 https://doi.org/10.1016/j.gene.2004.11.043
    23 https://doi.org/10.1016/j.jmb.2004.10.082
    24 https://doi.org/10.1016/j.jmb.2005.03.011
    25 https://doi.org/10.1016/j.pbi.2004.11.008
    26 https://doi.org/10.1016/j.tibs.2003.08.005
    27 https://doi.org/10.1016/j.tibs.2004.07.001
    28 https://doi.org/10.1016/s0092-8674(04)00127-8
    29 https://doi.org/10.1016/s0960-9822(01)00401-8
    30 https://doi.org/10.1046/j.1432-1033.2002.02970.x
    31 https://doi.org/10.1073/pnas.0401799101
    32 https://doi.org/10.1073/pnas.112063799
    33 https://doi.org/10.1073/pnas.172391199
    34 https://doi.org/10.1073/pnas.95.4.1460
    35 https://doi.org/10.1093/bioinformatics/bti1113
    36 https://doi.org/10.1093/nar/29.5.1034
    37 https://doi.org/10.1093/nar/9.1.133
    38 https://doi.org/10.1093/nar/gkg438
    39 https://doi.org/10.1093/nar/gkg595
    40 https://doi.org/10.1093/nar/gkg599
    41 https://doi.org/10.1093/nar/gkg938
    42 https://doi.org/10.1093/nar/gkh706
    43 https://doi.org/10.1093/nar/gkh841
    44 https://doi.org/10.1093/nar/gnh076
    45 https://doi.org/10.1101/gad.1184404
    46 https://doi.org/10.1101/gad.862301
    47 https://doi.org/10.1101/gr.2094104
    48 https://doi.org/10.1126/science.1103388
    49 https://doi.org/10.1126/science.1108625
    50 https://doi.org/10.1126/science.2468181
    51 https://doi.org/10.1137/0135006
    52 https://doi.org/10.1146/annurev.genet.34.1.499
    53 https://doi.org/10.1261/rna.5248604
    54 https://doi.org/10.1529/biophysj.103.020743
    55 schema:datePublished 2006-01
    56 schema:datePublishedReg 2006-01-01
    57 schema:description BACKGROUND: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. METHODS: The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. RESULTS: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.
    58 schema:genre research_article
    59 schema:inLanguage en
    60 schema:isAccessibleForFree true
    61 schema:isPartOf N4c47aff6f77c4abfbc82075afc463c8e
    62 Ne13e24c537df476aa09eeb24cdc8ee97
    63 sg:journal.1036449
    64 schema:name Partition function and base pairing probabilities of RNA heterodimers
    65 schema:pagination 3
    66 schema:productId N3146dad184ed456ea5d0483b63a2984f
    67 N6008aa0547dc4d9abb4a467882ec8f13
    68 N64f51315cd0e48f79f9d0739489c33e0
    69 N79274db162bb4d50a43ffbf89cb67a2a
    70 N980c7dbf7f2643308f783db3d209eac4
    71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049447594
    72 https://doi.org/10.1186/1748-7188-1-3
    73 schema:sdDatePublished 2019-04-10T13:18
    74 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    75 schema:sdPublisher Ndaaa4d6f0b6d445b9fc7ed5ccc1040a9
    76 schema:url http://link.springer.com/10.1186%2F1748-7188-1-3
    77 sgo:license sg:explorer/license/
    78 sgo:sdDataset articles
    79 rdf:type schema:ScholarlyArticle
    80 N0faef675bd414b3f9542960b23909918 rdf:first sg:person.0755677032.58
    81 rdf:rest Naa46084a7fb64b258df6ea322e11bc99
    82 N3146dad184ed456ea5d0483b63a2984f schema:name nlm_unique_id
    83 schema:value 101265088
    84 rdf:type schema:PropertyValue
    85 N49533efaec064894a803184546451484 rdf:first sg:person.01110764033.35
    86 rdf:rest Nd12153fbb56e4a43b3de05f0e9a97c75
    87 N4c47aff6f77c4abfbc82075afc463c8e schema:volumeNumber 1
    88 rdf:type schema:PublicationVolume
    89 N4f8115f2d76745b4990e296629f68162 rdf:first sg:person.0753447607.17
    90 rdf:rest N0faef675bd414b3f9542960b23909918
    91 N6008aa0547dc4d9abb4a467882ec8f13 schema:name pubmed_id
    92 schema:value 16722605
    93 rdf:type schema:PropertyValue
    94 N64f51315cd0e48f79f9d0739489c33e0 schema:name doi
    95 schema:value 10.1186/1748-7188-1-3
    96 rdf:type schema:PropertyValue
    97 N79274db162bb4d50a43ffbf89cb67a2a schema:name readcube_id
    98 schema:value eb8ec5170e7f5415cded7983c63f64c00529cf01318e42ea3c75d3b9f41e6ddd
    99 rdf:type schema:PropertyValue
    100 N980c7dbf7f2643308f783db3d209eac4 schema:name dimensions_id
    101 schema:value pub.1049447594
    102 rdf:type schema:PropertyValue
    103 Naa46084a7fb64b258df6ea322e11bc99 rdf:first sg:person.0612150527.13
    104 rdf:rest N49533efaec064894a803184546451484
    105 Nd12153fbb56e4a43b3de05f0e9a97c75 rdf:first sg:person.0664150133.70
    106 rdf:rest Nfacdc4140b1b42eeb9a78978de543324
    107 Ndaaa4d6f0b6d445b9fc7ed5ccc1040a9 schema:name Springer Nature - SN SciGraph project
    108 rdf:type schema:Organization
    109 Ne13e24c537df476aa09eeb24cdc8ee97 schema:issueNumber 1
    110 rdf:type schema:PublicationIssue
    111 Nfacdc4140b1b42eeb9a78978de543324 rdf:first sg:person.01222322364.52
    112 rdf:rest rdf:nil
    113 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    114 schema:name Biological Sciences
    115 rdf:type schema:DefinedTerm
    116 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    117 schema:name Biochemistry and Cell Biology
    118 rdf:type schema:DefinedTerm
    119 sg:journal.1036449 schema:issn 1748-7188
    120 schema:name Algorithms for Molecular Biology
    121 rdf:type schema:Periodical
    122 sg:person.01110764033.35 schema:affiliation https://www.grid.ac/institutes/grid.10420.37
    123 schema:familyName Flamm
    124 schema:givenName Christoph
    125 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110764033.35
    126 rdf:type schema:Person
    127 sg:person.01222322364.52 schema:affiliation https://www.grid.ac/institutes/grid.10420.37
    128 schema:familyName Hofacker
    129 schema:givenName Ivo L
    130 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01222322364.52
    131 rdf:type schema:Person
    132 sg:person.0612150527.13 schema:affiliation https://www.grid.ac/institutes/grid.10420.37
    133 schema:familyName Mückstein
    134 schema:givenName Ulrike
    135 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0612150527.13
    136 rdf:type schema:Person
    137 sg:person.0664150133.70 schema:affiliation https://www.grid.ac/institutes/grid.209665.e
    138 schema:familyName Stadler
    139 schema:givenName Peter F
    140 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0664150133.70
    141 rdf:type schema:Person
    142 sg:person.0753447607.17 schema:affiliation https://www.grid.ac/institutes/grid.10420.37
    143 schema:familyName Bernhart
    144 schema:givenName Stephan H
    145 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0753447607.17
    146 rdf:type schema:Person
    147 sg:person.0755677032.58 schema:affiliation https://www.grid.ac/institutes/grid.10420.37
    148 schema:familyName Tafer
    149 schema:givenName Hakim
    150 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755677032.58
    151 rdf:type schema:Person
    152 sg:pub.10.1007/bf00818163 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032495505
    153 https://doi.org/10.1007/bf00818163
    154 rdf:type schema:CreativeWork
    155 sg:pub.10.1007/bf02459506 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052391942
    156 https://doi.org/10.1007/bf02459506
    157 rdf:type schema:CreativeWork
    158 sg:pub.10.1016/j.thbio.2005.01.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022966750
    159 https://doi.org/10.1016/j.thbio.2005.01.002
    160 rdf:type schema:CreativeWork
    161 sg:pub.10.1016/s0092-8240(84)80062-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1054614704
    162 https://doi.org/10.1016/s0092-8240(84)80062-2
    163 rdf:type schema:CreativeWork
    164 sg:pub.10.1038/nature02871 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043341870
    165 https://doi.org/10.1038/nature02871
    166 rdf:type schema:CreativeWork
    167 sg:pub.10.1038/nbt1144 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028917438
    168 https://doi.org/10.1038/nbt1144
    169 rdf:type schema:CreativeWork
    170 sg:pub.10.1038/nrg1321 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013684976
    171 https://doi.org/10.1038/nrg1321
    172 rdf:type schema:CreativeWork
    173 sg:pub.10.1038/nrg1328 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019747892
    174 https://doi.org/10.1038/nrg1328
    175 rdf:type schema:CreativeWork
    176 sg:pub.10.1038/nsb0398-174 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045619143
    177 https://doi.org/10.1038/nsb0398-174
    178 rdf:type schema:CreativeWork
    179 sg:pub.10.1186/1471-2105-5-104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028464672
    180 https://doi.org/10.1186/1471-2105-5-104
    181 rdf:type schema:CreativeWork
    182 https://app.dimensions.ai/details/publication/pub.1083073479 schema:CreativeWork
    183 https://doi.org/10.1002/(sici)1097-0282(199902)49:2<145::aid-bip4>3.0.co;2-g schema:sameAs https://app.dimensions.ai/details/publication/pub.1025101661
    184 rdf:type schema:CreativeWork
    185 https://doi.org/10.1002/bies.10332 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034594169
    186 rdf:type schema:CreativeWork
    187 https://doi.org/10.1002/bip.360290621 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032289021
    188 rdf:type schema:CreativeWork
    189 https://doi.org/10.1002/cbic.200400219 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016880030
    190 rdf:type schema:CreativeWork
    191 https://doi.org/10.1002/jcc.10296 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051970143
    192 rdf:type schema:CreativeWork
    193 https://doi.org/10.1006/jmbi.1998.2436 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030245324
    194 rdf:type schema:CreativeWork
    195 https://doi.org/10.1006/jmbi.1999.2700 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034604829
    196 rdf:type schema:CreativeWork
    197 https://doi.org/10.1016/j.gene.2004.11.043 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018808147
    198 rdf:type schema:CreativeWork
    199 https://doi.org/10.1016/j.jmb.2004.10.082 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023879738
    200 rdf:type schema:CreativeWork
    201 https://doi.org/10.1016/j.jmb.2005.03.011 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032159466
    202 rdf:type schema:CreativeWork
    203 https://doi.org/10.1016/j.pbi.2004.11.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035292807
    204 rdf:type schema:CreativeWork
    205 https://doi.org/10.1016/j.tibs.2003.08.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005576380
    206 rdf:type schema:CreativeWork
    207 https://doi.org/10.1016/j.tibs.2004.07.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022439096
    208 rdf:type schema:CreativeWork
    209 https://doi.org/10.1016/s0092-8674(04)00127-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008587641
    210 rdf:type schema:CreativeWork
    211 https://doi.org/10.1016/s0960-9822(01)00401-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021943538
    212 rdf:type schema:CreativeWork
    213 https://doi.org/10.1046/j.1432-1033.2002.02970.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1001442923
    214 rdf:type schema:CreativeWork
    215 https://doi.org/10.1073/pnas.0401799101 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026962739
    216 rdf:type schema:CreativeWork
    217 https://doi.org/10.1073/pnas.112063799 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040956624
    218 rdf:type schema:CreativeWork
    219 https://doi.org/10.1073/pnas.172391199 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018259290
    220 rdf:type schema:CreativeWork
    221 https://doi.org/10.1073/pnas.95.4.1460 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009187647
    222 rdf:type schema:CreativeWork
    223 https://doi.org/10.1093/bioinformatics/bti1113 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049107232
    224 rdf:type schema:CreativeWork
    225 https://doi.org/10.1093/nar/29.5.1034 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005082622
    226 rdf:type schema:CreativeWork
    227 https://doi.org/10.1093/nar/9.1.133 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004222010
    228 rdf:type schema:CreativeWork
    229 https://doi.org/10.1093/nar/gkg438 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025084080
    230 rdf:type schema:CreativeWork
    231 https://doi.org/10.1093/nar/gkg595 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013618001
    232 rdf:type schema:CreativeWork
    233 https://doi.org/10.1093/nar/gkg599 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017511013
    234 rdf:type schema:CreativeWork
    235 https://doi.org/10.1093/nar/gkg938 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007345576
    236 rdf:type schema:CreativeWork
    237 https://doi.org/10.1093/nar/gkh706 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053499486
    238 rdf:type schema:CreativeWork
    239 https://doi.org/10.1093/nar/gkh841 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016061119
    240 rdf:type schema:CreativeWork
    241 https://doi.org/10.1093/nar/gnh076 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046119255
    242 rdf:type schema:CreativeWork
    243 https://doi.org/10.1101/gad.1184404 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024436325
    244 rdf:type schema:CreativeWork
    245 https://doi.org/10.1101/gad.862301 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000961502
    246 rdf:type schema:CreativeWork
    247 https://doi.org/10.1101/gr.2094104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050487471
    248 rdf:type schema:CreativeWork
    249 https://doi.org/10.1126/science.1103388 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042123507
    250 rdf:type schema:CreativeWork
    251 https://doi.org/10.1126/science.1108625 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046921907
    252 rdf:type schema:CreativeWork
    253 https://doi.org/10.1126/science.2468181 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062538914
    254 rdf:type schema:CreativeWork
    255 https://doi.org/10.1137/0135006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062839734
    256 rdf:type schema:CreativeWork
    257 https://doi.org/10.1146/annurev.genet.34.1.499 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031435901
    258 rdf:type schema:CreativeWork
    259 https://doi.org/10.1261/rna.5248604 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034010998
    260 rdf:type schema:CreativeWork
    261 https://doi.org/10.1529/biophysj.103.020743 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023790799
    262 rdf:type schema:CreativeWork
    263 https://www.grid.ac/institutes/grid.10420.37 schema:alternateName University of Vienna
    264 schema:name Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04170, Leipzig, Germany
    265 Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, Vienna, Austria
    266 rdf:type schema:Organization
    267 https://www.grid.ac/institutes/grid.209665.e schema:alternateName Santa Fe Institute
    268 schema:name Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16–18, D-04170, Leipzig, Germany
    269 The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, New Mexico
    270 Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, Vienna, Austria
    271 rdf:type schema:Organization
     




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


    ...