On the Number of Saturated and Optimal Extended 2-Regular Simple Stacks in the Nussinov-Jacobson Energy Model.

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  • Author(s): Guo Q;Guo Q; Jin Y; Jin Y; Li M; Li M; Sun LH; Sun LH; Xu Y; Xu Y
  • Source:
    Journal of computational biology : a journal of computational molecular cell biology [J Comput Biol] 2022 May; Vol. 29 (5), pp. 425-440. Date of Electronic Publication: 2022 Mar 28.
  • Publication Type:
    Journal Article; Research Support, Non-U.S. Gov't
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Mary Ann Liebert, Inc Country of Publication: United States NLM ID: 9433358 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1557-8666 (Electronic) Linking ISSN: 10665277 NLM ISO Abbreviation: J Comput Biol Subsets: MEDLINE
    • Publication Information:
      Original Publication: New York, NY : Mary Ann Liebert, Inc., c1994-
    • Subject Terms:
      Proteins*/chemistry ; RNA*/chemistry; Algorithms ; Base Pairing ; Models, Molecular ; Nucleic Acid Conformation
    • Abstract:
      It is known that both RNA secondary structure and protein contact map can be presented using combinatorial diagrams, the combinatorial enumeration and related problems of which have been studied extensively. Motivated by previous enumeration works on saturated RNA secondary structures and extended stack structures of protein contact maps, we are interested in the enumeration problems of saturated and optimal extended stacks in the Nussinov-Jacobson energy model, in which each base pair contributes energy -1. Then optimal structures are those with most arcs, and locally optimal structures are exactly the saturated structures, in which no more arcs can be added without violating the structure definition. For saturated extended 2-regular simple stacks, whose degree configuration is related to the protein fold in two-dimensional honeycomb lattice, we obtain generating function equation and asymptotic formula for its number. Moreover, an explicit formula for the number of optimal extended 2-regular simple stacks is also obtained.
    • Contributed Indexing:
      Keywords: RNA secondary structure; combinatorial enumeration; protein contact map; saturated stacks
    • Accession Number:
      0 (Proteins)
      63231-63-0 (RNA)
    • Publication Date:
      Date Created: 20220330 Date Completed: 20230601 Latest Revision: 20230601
    • Publication Date:
      20240104
    • Accession Number:
      10.1089/cmb.2021.0421
    • Accession Number:
      35353583