bpfold / README.md

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datasets:
  - RNAStrAlign
  - bpRNA
language: rna
library_name: multimolecule
license: agpl-3.0
pipeline: rna-secondary-structure
pipeline_tag: other
tags:
  - Biology
  - RNA
widget:
  - example_title: microRNA 21
    output:
      text: ((((()[[{<)<))(]]}>>))
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: UAGCUUAUCAGACUGAUGUUGA
  - example_title: microRNA 146a
    output:
      text: ((([.{<{.()A)])}}()>a)
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: UGAGAACUGAAUUCCAUGGGUU
  - example_title: microRNA 155
    output:
      text: (()()([[(){{{..<)]]}}}>)
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: UUAAUGCUAAUCGUGAUAGGGGUU
  - example_title: RNA component of mitochondrial RNA processing endoribonuclease
    output:
      text: >-
        ((((((((()[()()))))))))(((((([{(([)]{[{[[[[[)]]]]]]}()()(){()))))))(((]()[)))((()}[{())({](([)][)[<)(((((](<)]})))))>>(})((()()((()()([)([(([){()<A()(])()([)]B()()<()))]}()>>]()a))()())[)()b(()(()[)())()()(()()]({))()][([)][[[[)(([)]]()()()(})())()]]].()(])}([)]()](])}()()()()
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      GGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUAAAAAAAAA
  - example_title: 7SK small nuclear RNA
    output:
      text: >-
        (()((((()()(()())()()([){](()[)()((()([((([()){))){))]([<}()}{A)]>.]()}a()()]()(()([)])().()()(()[)))]))())([[)](.)()()()()(()((([{([)])]})))({)()()(<ABBB]([((((()))})))][)>abbb]()(()[)()()(][)]()([})]()([)()]()()(()()()([[().()[()(){)(]()()}(){()({))()]]()[})()()()(()())]()()([[{{<())]]}}(}>()()()()())([[)(()({<<{]])}})>>()()()()
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      GGAUGUGAGGGCGAUCUGGCUGCGACAUCUGUCACCCCAUUGAUCGCCAGGGUUGAUUCGGCUGAUCUGGCUGGCUAGGCGGGUGUCCCCUUCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGCGCUCGGUCGAAGAGGACGACCAUCCCCGAUAGAGGAGGACCGGUCUUCGGUCAAGGGUAUACGAGUAGCUGCGCUCCCCUGCUAGAACCUCCAAACAAGCUCUCAAGGUCCAUUUGUAGGAGAACGUAGGGUAGUCAAGCUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGCAUGUGGCAGUCUGCCUUUCUUUU
  - example_title: telomerase RNA component
    output:
      text: >-
        (([[{<())(]()(()(()[()[[{()[[()[[[[[(()()()(()[)(()()){([)]]()[[[[([[[[[)<[[)((((()(()()()(([)]([(()(})()(){{{))(){<][)]())()()))))(])]]]]]]()]]]]())(()(())(())()()()()()()}()([)]}}}()>()]]]]>]()(])]()]]()]()()()[((())(()()(()[)()({[[(){)()(()([[()[(){{{[(((((((()[[{{{{<)()(()()])()()}}}}()]>[))))))()({)<A)()]}()>()a]()]]]()}}}.()()()])()}()]])()()}[()()()){]()())}]()()([)((){()<<{{{{{{()(<(<)A)A{{{{{(){{{{{{])()}}}}}}}}}}}}>a>a()}}}}}}>>})})][)]>
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC
  - example_title: vault RNA 2-1
    output:
      text: >-
        ((((([()({)<[[[[[)([[()()[()()[)([([{(((((()[()(){<)))))]<)][)]}(]]<<<][).]}(>>>]]]]])(](){)].])))[()>}>)}>]
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      CGGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUUAUGCAA
  - example_title: brain cytoplasmic RNA 1
    output:
      text: >-
        (((([[[([[())()()[(([)[[)[()((((((([)]))))))))))]]](()]()[)]]()(()()([{{{{{{{{{())(]}}()(]}}}}}}})([)][[)]((]()()[()))()(]()[)(()())()()()()(]()([))(((())()(){){([))()]()()]}(}()()())()()()()]]]]()())
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: >-
      GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCUCUCAGGGAGGCUAAGAGGCGGGAGGAUAGCUUGAGCCCAGGAGUUCGAGACCUGCCUGGGCAAUAUAGCGAGACCCCGUUCUCCAGAAAAAGGAAAAAAAAAAACAAAAGACAAAAAAAAAAUAAGCGUAACUUCCCUCAAAGCAACAACCCCCCCCCCCCUUU
  - example_title: HIV-1 TAR-WT
    output:
      text: (((([[[[([[[[[[([[[[){{<<<<<])[})}>>>>>]]]]]]]]]].]]]])))
    pipeline_tag: rna-secondary-structure
    sequence_type: ncRNA
    task: rna-secondary-structure
    text: GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACC
  - example_title: prion protein (Kanno blood group)
    output:
      text: (([[[{()<)()(((<]}[()[[)({()][[[)(A((]]]AA}))){{{(])>))]a>a]]}}})a
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: AUGGCGAACCUUGGCUGCUGGAUGCUGGUUCUCUUUGUGGCCACAUGGAGUGACCUGGGCCUCUGC
  - example_title: interleukin 10
    output:
      text: ([[[)((((){{]]]([[[{<{)()]A(}BB[A)}<())]]}}>()))]>aabb
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: AUGCACAGCUCAGCACUGCUCUGUUGCCUGGUCCUCCUGACUGGGGUGAGGGCC
  - example_title: Zaire ebolavirus
    output:
      text: >-
        (((((()())))))()([)]()(([)]()()((())()()()([[(){{)(()(())]]})(})([.)](())()([)](((([){()]()()()()))()(()([<}{())]>())(()[[())({)(()<({])}())}()>([)(])]()(})(()[)]()[)]()(([()))()(({[)()](])()(()[())<()})((()())([){](()()]()))>}()()()()()()()()()()(())((.)()[)](()[())]()()[()()()())((())[[)](]()(])()))()()
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AAUGUUCAAACACUUUGUGAAGCUCUGUUAGCUGAUGGUCUUGCUAAAGCAUUUCCUAGCAAUAUGAUGGUAGUCACAGAGCGUGAGCAAAAAGAAAGCUUAUUGCAUCAAGCAUCAUGGCACCACACAAGUGAUGAUUUUGGUGAGCAUGCCACAGUUAGAGGGAGUAGCUUUGUAACUGAUUUAGAGAAAUACAAUCUUGCAUUUAGAUAUGAGUUUACAGCACCUUUUAUAGAAUAUUGUAACCGUUGCUAUGGUGUUAAGAAUGUUUUUAAUUGGAUGCAUUAUACAAUCCCACAGUGUUAU
  - example_title: SARS coronavirus
    output:
      text: >-
        (([{()[))(]]())()(())}()((([)]([{)]}()([[)](()()()()())([(()((()())[)(][)]){())](()())()([)]}(())([)]()(][)]([)]()()()()()(()(()[([[)(()())()]{{][[([)][)]()]<(())}()]]()(()()())[()()(()[{)][)}()>}()((()()()]]()([[)](()(][)])([())([){]()]))(})(()((()))()[)()((()[)]{()()])()([)([)}()]]()(((())(()([))()(()()()]()[[)]]()())()(())()[[[[[)]()()]]]()(())()().()()(())(())(())()({)(([))](])()(()[)()]([)](}([))]()()([).([{)]()(])()((()()()))(([)]((}))[)](([))(])()()((()(())()).())(([)[(){)]))]}([)]()
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AUGUUUAUUUUCUUAUUAUUUCUUACUCUCACUAGUGGUAGUGACCUUGACCGGUGCACCACUUUUGAUGAUGUUCAAGCUCCUAAUUACACUCAACAUACUUCAUCUAUGAGGGGGGUUUACUAUCCUGAUGAAAUUUUUAGAUCAGACACUCUUUAUUUAACUCAGGAUUUAUUUCUUCCAUUUUAUUCUAAUGUUACAGGGUUUCAUACUAUUAAUCAUACGUUUGACAACCCUGUCAUACCUUUUAAGGAUGGUAUUUAUUUUGCUGCCACAGAGAAAUCAAAUGUUGUCCGUGGUUGGGUUUUUGGUUCUACCAUGAACAACAAGUCACAGUCGGUGAUUAUUAUUAACAAUUCUACUAAUGUUGUUAUACGAGCAUGUAACUUUGAAUUGUGUGACAACCCUUUCUUUGCUGUUUCUAAACCCAUGGGUACACAGACACAUACUAUGAUAUUCGAUAAUGCAUUUAAAUGCACUUUCGAGUACAUAUCU
  - example_title: insulin
    output:
      text: >-
        ([()()()[)()()([)()((){((){([{[{)[)]((<]}(((((]}<))))])()[A}()>())(]a)()()([))()()>(])()([)](())(([([)({)(])){)]()([)]}()}()([)](()()()(()()[())()([[)]({)()(){((){(()<()A())][[())()})}>()}()()(]())()a(()(()[()(()()()()[)(]()){<())])}>()()]()()([(){()()<())]()}(()([)>()][())(()())()([{)](<()<}{)]]>}(>)()([)(())(](()))()())()(]}]().)
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AUGGCCCUGUGGAUGCGCCUCCUGCCCCUGCUGGCGCUGCUGGCCCUCUGGGGACCUGACCCAGCCGCAGCCUUUGUGAACCAACACCUGUGCGGCUCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCCCUUGGCCCUGGAGGGGUCCCUGCAGAAGCGUGGCAUUGUGGAACAAUGCUGUACCAGCAUCUGCUCCCUCUACCAGCUGGAGAACUACUGCAACUAG
  - example_title: cyclin dependent kinase inhibitor 2A
    output:
      text: >-
        ((((()))))(())()()(()(()()())(()()())()((([{<)]}[{ABB[>)(<)]]}ab>b()()()[{{)(())()((<())[)()((){()())()()]()(()]()())()(()}}([){]()([{<)())()(]([}()[))>}]((())])((([.(){)))(([)]{][<A((([{)]}[))]B[)]()(})]>a}b()()()([)]()(()()>())([)][)()([<())](()([{)]}(((()[{(){{())()()][()})([)}[[[()<(()))]]]}()]]()()}>(())(()[(){([)])]}([(())())](([))(()()()>)()()()()(){(()()()](()([))){()][)]()}}()([([)](()))](()()()[())()(()](])()()()(()[{)())]([<A(})())]()>a()()()((()()()[())])
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AUGGAGCCGGCGGCGGGGAGCAGCAUGGAGCCUUCGGCUGACUGGCUGGCCACGGCCGCGGCCCGGGGUCGGGUAGAGGAGGUGCGGGCGCUGCUGGAGGCGGGGGCGCUGCCCAACGCACCGAAUAGUUACGGUCGGAGGCCGAUCCAGGUCAUGAUGAUGGGCAGCGCCCGAGUGGCGGAGCUGCUGCUGCUCCACGGCGCGGAGCCCAACUGCGCCGACCCCGCCACUCUCACCCGACCCGUGCACGACGCUGCCCGGGAGGGCUUCCUGGACACGCUGGUGGUGCUGCACCGGGCCGGGGCGCGGCUGGACGUGCGCGAUGCCUGGGGCCGUCUGCCCGUGGACCUGGCUGAGGAGCUGGGCCAUCGCGAUGUCGCACGGUACCUGCGCGCGGCUGCGGGGGGCACCAGAGGCAGUAACCAUGCCCGCAUAGAUGCCGCGGAAGGUCCCUCAGACAUCCCCGAUUGA
  - example_title: human papillomavirus type 16 E6
    output:
      text: >-
        (((()()()(([)]()([{)()]}())((()[(){))(((][}({))))(()<]()}()[)](()[[{[(A))>(]]}{{()(()(([)])]([(((())[)]))]()([)][)][)}}a]()(())((()[))({)]}([)(()]([)][{{)()]}()()()()()()(}()())(()([)]([)([[[.())]]]({([{)])]([)]([[(){{<)A]()}}>()]())a()()()(([)(}[)]()((<()}()))([)](()[)]{]()()(())>()[[(){)]}()]([)(])()()(())([)]()()(()()()}()([)]()()([)][()[[{<(A)B)]}(({[{())]()C>}(])(<)a()b())(()()c{)()(])()}}()()([)()()()>()()()(([{))]}(([))(])(()(()()(()())[)())]([)]({{)()]()()}}(()))))
    pipeline_tag: rna-secondary-structure
    sequence_type: mRNA
    task: rna-secondary-structure
    text: >-
      AUGCACCAAAAGAGAACUGCAAUGUUUCAGGACCCACAGGAGCGACCCAGAAAGUUACCACAGUUAUGCACAGAGCUGCAAACAACUAUACAUGAUAUAAUAUUAGAAUGUGUGUACUGCAAGCAACAGUUACUGCGACGUGAGGUAUAUGACUUUGCUUUUCGGGAUUUAUGCAUAGUAUAUAGAGAUGGGAAUCCAUAUGCUGUAUGUGAUAAAUGUUUAAAGUUUUAUUCUAAAAUUAGUGAGUAUAGACAUUAUUGUUAUAGUUUGUAUGGAACAACAUUAGAACAGCAAUACAACAAACCGUUGUGUGAUUUGUUAAUUAGGUGUAUUAACUGUCAAAAGCCACUGUGUCCUGAAGAAAAGCAAAGACAUCUGGACAAAAAGCAAAGAUUCCAUAAUAUAAGGGGUCGGUGGACCGGUCGAUGUAUGUCUUGUUGCAGAUCAUCAAGAACACGUAGAGAAACCCAGCUGUAA
  - example_title: NRAS proto-oncogene
    output:
      text: >-
        ((((((()([[)(())()()(){({)()()()<()]}]()[))))))]()()([<A()}{().)].>a()(([)().()[}()({{{{()<()))]]}()}}}>()()(()()()()>()[{(()))]}()
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      GGGGCCGGAAGUGCCGCUCCUUGGUGGGGGCUGUUCAUGGCGGUUCCGGGGUCUCCAACAUUUUUCCCGGCUGUGGUCCUAAAUCUGUCCAAAGCAGAGGCAGUGGAGCUUGAGGUUCUUGCUGGUGUGAA
  - example_title: amyloid beta precursor protein
    output:
      text: >-
        ([{()(){()()()[)({(){{())]}(})(])}(()[()[(([)]()[[())()()]])(]()[{[<)](()AA])}((>)()a)a([()()(((([(())()))))]{)(({)][)}]}([)]((])[[)]()(]([)]})()()}()
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      GUCAGUUUCCUCGGCAGCGGUAGGCGAGAGCACGCGGAGGAGCGUGCGCGGGGGCCCCGGGAGACGGCGGCGGUGGCGGCGCGGGCAGAGCAAGGACGCGGCGGAUCCCACUCGCACAGCAGCGCACUCGGUGCCCCGCGCAGGGUCGCG
  - example_title: RUNX family transcription factor 1
    output:
      text: >-
        ([({()()())())()]()}()(()([)[)((((((([[[[[[)([[[{()<)([)]((]A}]]>))()]]]]]][)])))))](][)()](())((()[)([)][)()(((]a[[[[[{()(<()))))]((]]]]][}([()>)))()]](()()())()()(((()))()([)(({()))]()}()()())
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      ACUUCUUUGGGCCUCAUAAACAACCACAGAACCACAAGUUGGGUAGCCUGGCAGUGUCAGAAGUCUGAACCCAGCAUAGUGGUCAGCAGGCAGGACGAAUCACACUGAAUGCAAACCACAGGGUUUCGCAGCGUGGUAAAAGAAAUCAUUGAGUCCCCCGCCUUCAGAAGAGGGUGCAUUUUCAGGAGGAAGCG
  - example_title: fragile X messenger ribonucleoprotein 1
    output:
      text: >-
        (([(((){()[{))]}()(((([())))()(){(())()[{())()()()()()(((]}()([{)]()()}()([[)({[)]]]((((([[)([(}){)]<}{({)(]])))))()()()(})([{)](([)(}[)([{)]}(][)(]{)(([{)]}[[{().[<)(({])})([{)]}]}]([{)]}({])}}(()>()>))}{([()()<)]{(A)()])))()}(}())(()()[[)](>a])()()()<)}]})()>
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      CUCAGUCAGGCGCUCAGCUCCGUUUCGGUUUCACUUCCGGUGGAGGGCCGCCUCUGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGCGGCGGUGACGGAGGCGCCGCUGCCAGGGGGCGUGCGGCAGCGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCUGGGCCUCGAGCGCCCGCAGCCCACCUCUCGGGGGCGGGCUCCCGGCGCUAGCAGGGCUGAAGAGAAG
  - example_title: MYC proto-oncogene
    output:
      text: >-
        ([{{{{{{{)({])}()(}}}}}}}[)()()(()(])())([())(())(()[())()(()(){)]()()((([[[[){()]]]))]([)()()((([)(){]()))()(()[[[[)]()}()()((((}((((]()))))]))))()()]]()()()()()([())](()(()()))(()()(()))()()(()[()(()[)(){[)]({])((()}<()([()())]]()()()(()(})[)][{))(AA()()(([)]B[)]B]}>).aa(()()b()()b()}[{[[[)()((]]]]}([)[()[))()(())()]()]]()((()[{))]()}()([)]()()](())(())()()()
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      AACUCGCUGUAGUAAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGCCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUGAUCCCCCAGCCAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGCACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUAUUCUGCCCAUUUGGGGACACUUCCCCGCCGCUGCCAGGACCCGCUUCUCUGAAAGGCUCUCCUUGCAGCUGCUUAGACG
  - example_title: activating transcription factor 4
    output:
      text: >-
        (()([())]()([{()<()([)]{)]}(())(()([)]([)]([)](})()()()((())()()((((([))))))([)()()](({<)([)]A]}>)()((([[){{))()]]()(})}(()()()(()[))](())()(([[)(]{{((([[[)]]]))]())()}()()}(((((()())))))()[)]()([({)()).()(]([<)]((.[()[))]}()(){>)()(((])()()})()())()([)]()()(([{()<))]a}()>>)()()())
    pipeline_tag: rna-secondary-structure
    sequence_type: 5' UTR
    task: rna-secondary-structure
    text: >-
      CAUUUCUACUUUGCCCGCCCACAGAUGUAGUUUUCUCUGCGCGUGUGCGUUUUCCCUCCUCCCCGCCCUCAGGGUCCACGGCCACCAUGGCGUAUUAGGGGCAGCAGUGCCUGCGGCAGCAUUGGCCUUUGCAGCGGCGGCAGCAGCACCAGGCUCUGCAGCGGCAACCCCCAGCGGCUUAAGCCAUGGCGCUUCUCACGGCAUUCAGCAGCAGCGUUGCUGUAACCGACAAAGACACCUUCGAAUUAAGCACAUUCCUCGAUUCCAGCAAAGCACCGCAAC
  - example_title: Human GPI protein p137
    output:
      text: >-
        (((()()))()()()(()(())()[)()]([{)]}(())(()()()(()()(([()))(){)()]())(())}()([)]()()(([())][[[[[[[[())]]]]]]]]()([()([)[)(]()())]()(([{)()(.)())]()()(()({()){])}()}}()()(())([)(()[()[[{)(())]](]()([{)(]}([<)()A)AAA)().]()()(}[>[)]]()(([)]aaa())()()(a()()[)]((()()(][)]())([)]([{))()](})()([[)]]()()())
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      UUUUUAAAAGGAAAAGAUACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUUUGAAAGGCACCAGUAUGUGUUUUAGAUUGAUUUAAAUGUUUCAUUUAAAUCACGGACAGUAGUUUCAGUUCUGAUGGUAUAAGCAAAACAAAUAAAACGUUUAUAAAAGUUGUAUCUUGAAACACUGGUGUUCAACAGCUAGCAGCUUAUGUGAUUCACCCCAUGCCACGUUAGUGUCACAAAUUUUAUGGUUUAUCUCCAGCAACAUUUCUCUAGUACUUGCACUUAUUAUCUGAAUUC
  - example_title: nucleophosmin 1
    output:
      text: >-
        (([{()()())]()()(()[)()()]()(())(()[)(()((){[)()(](])[<<<(())}[)](]())>>>()(()())(())([[)(([))()]()()())](()](((()([)()))(())[())(){]<])()}()()>()([)]()([()()())]()([())()()(()()([)(]](.[)())()[)()].()()()()()(([))(])()()](()[{)]}(()((([)([{)]}[)()(())((])({{(<()]))}}()()[))(()()[(>)[)]([)]()(])]()[)].([)()()()(]()[)(]([)][)()]}[())]
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      GAAAAUAGUUUAAACAAUUUGUUAAAAAAUUUUCCGUCUUAUUUCAUUUCUGUAACAGUUGAUAUCUGGCUGUCCUUUUUAUAAUGCAGAGUGAGAACUUUCCCUACCGUGUUUGAUAAAUGUUGUCCAGGUUCUAUUGCCAAGAAUGUGUUGUCCAAAAUGCCUGUUUAGUUUUUAAAGAUGGAACUCCACCCUUUGCUUGGUUUUAAGUAUGUAUGGAAUGUUAUGAUAGGACAUAGUAGUAGCGGUGGUCAGACAUGGAAAUGGUGGGGAGACAAAAAUAUACAUGUGAAAUAAAACUCAGUAUUUUAAUAAAGUAGCACGGUUUCUAUUGA
  - example_title: superoxide dismutase 1
    output:
      text: >-
        ((((()()()()))))((()[)]()()()()()([([[)](()][(){)<A{[)(]A](]()[)])}()}>(a)()(a()()[)](([)()[)()()(]{(<(()()([)]))]()()[[[[)}()>]]()()()()()(])(([)).()]({)(()[)](([{))()()(]})()([)(()]()())]()()([)}(()()()(({{[)[(){())<]()])([)()]}()]}}(()[()[)([)]()()(]{()()[)()(]>])()()}(()[)][[()[()[(){([)()]())()()]}]({(()(])())())}()()]()()()()([())(()]()[)()]()()
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      ACAUUCCCUUGGAUGUAGUCUGAGGCCCCUUAACUCAUCUGUUAUCCUGCUAGCUGUAGAAAUGUAUCCUGAUAAACAUUAAACACUGUAAUCUUAAAAGUGUAAUUGUGUGACUUUUUCAGAGUUGCUUUAAAGUACCUGUAGUGAGAAACUGAUUUAUGAUCACUUGGAAGAUUUGUAUAGUUUUAUAAAACUCAGUUAAAAUGUCUGUUUCAAUGACCUGUAUUUUGCCAGACUUAAAUCACAGAUGGGUAUUAAACUUGUCAGAAUUUCUUUGUCAUUCAAGCCUGUGAAUAAAAACCCUGUAUGGCACUUAUUAUGAGGCUAUUAAAAGAAUCCAAAUUCAAACUAAA
  - example_title: hemoglobin subunit alpha 2
    output:
      text: >-
        ((()[{{<()()<<AA.)()()]()(([B(([[[[[[[()(){<))]]]]]]](}())()()()}.{()[{)()(>())]]}(()[)()>()>aa()(.)}>()}))b]
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      CUGGAGCCUCGGUAGCCGUUCCUCCUGCCCGCUGGGCCUCCCAACGGGCCCUCCUCCCCUCCUUGCACCGGCCCUUCCUGGUCUUUGAAUAAAGUCUGAGUGGGCAGCA
  - example_title: BRAF proto-oncogene
    output:
      text: >-
        ((([()[)()([)]([)](){<()([)])()(]])()()()()()(()[)([{)](])(}())}(([)]([))()(()(()[)()(])]([)]())()()()()()([{)()>()]}([)]()([)]()()()([)(()]([)]()[()())()({())(()]()())(([()<)]}()())()()((>([{((())))]))(()}([(){{)])()(}}()[()()())([{{())(()()(])()}}(){)()(<)]()()()([())(})([())]>()()()](())()((.[)()[{()<<)]()}>>()](())()()(()(()[)(()))](()((()[[[{[{{))((]]]()))(<)}})}]()()([()([)[)()]](()]([)]((())[{)]()()()>}())())
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: >-
      AACAAAUGAGUGAGAGAGUUCAGGAGAGUAGCAACAAAAGGAAAAUAAAUGAACAUAUGUUUGCUUAUAUGUUAAAUUGAAUAAAAUACUCUCUUUUUUUUUAAGGUGAACCAAAGAACACUUGUGUGGUUAAAGACUAGAUAUAAUUUUUCCCCAAACUAAAAUUUAUACUUAACAUUGGAUUUUUAACAUCCAAGGGUUAAAAUACAUAGACAUUGCUAAAAAUUGGCAGAGCCUCUUCUAGAGGCUUUACUUUCUGUUCCGGGUUUGUAUCAUUCACUUGGUUAUUUUAAGUAGUAAACUUCAGUUUCUCAUGCAACUUUUGUUGCCAGCUAUCACAUGUCCACUAGGGACUCCAGAAGAAGACCCUACCUAUGCCUGUGUUUGCAGGUGAGAAGUUGGCAGUCGGUUAGCCUGGG
  - example_title: H3 clustered histone 1
    output:
      text: (([()((((((([)({][<[[[()())(}{]{{]{]][())..})}})))))>]})])
    pipeline_tag: rna-secondary-structure
    sequence_type: 3' UTR
    task: rna-secondary-structure
    text: UUACUGUGGUCUCUCUGACGGUCCAAGCAAAGGCUCUUUUCAGAGCCACCACCUUUUC

BPfold

Pre-trained model for RNA secondary structure prediction using base pair motif energy.

Disclaimer

This is an UNOFFICIAL implementation of Deep generalizable prediction of RNA secondary structure via base pair motif energy by Heqin Zhu, Fenghe Tang, Quan Quan, Ke Chen, Peng Xiong, and S. Kevin Zhou.

The OFFICIAL repository of BPfold is at heqin-zhu/BPfold.

The MultiMolecule implementation preserves the released BPfold architecture, base-pair motif energy feature construction, and canonical/non-canonical post-processing semantics.

The team releasing BPfold did not write this model card for this model so this model card has been written by the MultiMolecule team.

Model Details

BPfold predicts RNA base-pair contact maps from a single RNA sequence. It augments a transformer encoder with two L x L base-pair motif energy maps computed from three-neighbor base-pair motifs. MultiMolecule exposes BPfold as a single checkpoint and stores the motif-energy lookup tables inside it.

The model uses:

token order: follows the MultiMolecule tokenizer.
unknown bases: tokenized as N and treated as U during BPfold feature construction, matching the upstream fallback; padding follows attention_mask.
self-attention: dynamic position bias with adjacency bias from motif-energy maps.
pairwise convolutions: three residual 2D convolution layers over the adjacency maps before the transformer blocks.
post-processing: constrained refinement for canonical pairs, plus the optional BPfold non-canonical pass and mixed canonical/non-canonical outputs.

Model Specification

Num Layers	Hidden Size	Num Parameters (M)	FLOPs (G)	MACs (G)
12	256	47.77	87.78	42.74

FLOPs and MACs are computed with multimolecule.utils for one 600 nt sequence.

Usage

The model file depends on the multimolecule library. You can install it using pip:

pip install multimolecule

RNA Secondary Structure Pipeline

import multimolecule
from transformers import pipeline

predictor = pipeline("rna-secondary-structure", model="multimolecule/bpfold")
output = predictor("GGUAAAACAGCCUGU")

PyTorch Inference

from multimolecule import BpfoldModel, RnaTokenizer

tokenizer = RnaTokenizer.from_pretrained("multimolecule/bpfold")
model = BpfoldModel.from_pretrained("multimolecule/bpfold")
input = tokenizer("GGUAAAACAGCCUGU", return_tensors="pt")

output = model(**input)
contact_map = output.contact_map  # (1, L, L) base-pair probability matrix

Training Details

BPfold was trained for RNA secondary structure prediction with base-pair motif energy priors.

Training Data

RNAStrAlign: 37,149 RNAs from eight RNA families were filtered to remove redundant sequences and invalid secondary structures, yielding 29,647 unique RNAs. Sequences longer than 600 nt were removed for training, leaving 19,313 training RNAs.
bpRNA-1m: 102,318 RNAs from 2,588 families were deduplicated with CD-HIT at 80% sequence identity and split into TR0/TS0 with 12,114/1,305 RNAs.
evaluation data: ArchiveII contains 3,966 RNAs; Rfam12.3-14.10 contains 10,791 RNAs from 1,992 families; bpRNA-new contains 5,401 RNAs; PDB contains 116 high-resolution RNAs split into TS1/TS2/TS3.

Training Procedure

objective: binary cross entropy over base-pair contact maps.
optimizer: Adam.
learning rate: 5e-4.
training epochs: 150.
batch size: 48.
positive-class weight: 300.
batching: length-matching mini-batches to reduce padding.
sequence features: token embeddings converted to the MultiMolecule tokenizer order.
structural priors: two L x L energy maps from three-neighbor base-pair motifs.
post-processing: constrained refinement for canonical pairs, minimum loop length, non-overlapping pairs, and isolated-pair removal.

Citation

@article{zhu2025bpfold,
  title   = {Deep generalizable prediction of {RNA} secondary structure via base pair motif energy},
  author  = {Zhu, Heqin and Tang, Fenghe and Quan, Quan and Chen, Ke and Xiong, Peng and Zhou, S. Kevin},
  journal = {Nature Communications},
  volume  = {16},
  number  = {1},
  pages   = {5856},
  year    = {2025},
  doi     = {10.1038/s41467-025-60048-1},
  url     = {https://doi.org/10.1038/s41467-025-60048-1}
}

The artifacts distributed in this repository are part of the MultiMolecule project. If you use MultiMolecule in your research, you must cite the MultiMolecule project.

License

This model is licensed under the GNU Affero General Public License.

For additional terms and clarifications, please refer to our License FAQ.

SPDX-License-Identifier: AGPL-3.0-or-later

multimolecule
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bpfold

BPfold

Disclaimer

Model Details

Model Specification

Links

Usage

RNA Secondary Structure Pipeline

PyTorch Inference

Training Details

Training Data

Training Procedure

Citation

License