• PseudoViewer3

  • Referenced in 6 articles [sw17134]
  • drawings of large-scale RNA structures with pseudoknots. Motivation: Pseudoknots in RNA structures make visualization ... structures difficult. Even if a pseudoknot itself is represented without a crossing, visualization ... entire RNA structure with a pseudoknot often results in a drawing with crossings between ... pseudoknot and other structural elements, and requires additional intervention by the user to ensure that...
  • KineFold

  • Referenced in 9 articles [sw33134]
  • RNA/DNA folding path and structure prediction including pseudoknots and knots...
  • HotKnots

  • Referenced in 4 articles [sw17267]
  • Heuristic prediction of RNA secondary structures including pseudoknots. We present HotKnots, a new heuristic algorithm ... prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming ... using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate ... Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms...
  • IPknot

  • Referenced in 3 articles [sw17124]
  • accurate prediction of RNA secondary structures with pseudoknots using integer programming. Motivation: Pseudoknots found ... secondary structures cover certain classes of pseudoknotted structures, but only a few of them achieve ... method for predicting RNA secondary structures with pseudoknots based on maximizing expected accuracy ... predicted structure. IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures...
  • ProbKnot

  • Referenced in 2 articles [sw17268]
  • Fast prediction of RNA secondary structure including pseudoknots. It is a significant challenge to predict ... secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots of any topology ... four tested algorithms that are capable of pseudoknot prediction. The program is available for download...
  • TPstructure

  • Referenced in 3 articles [sw23814]
  • capable of generating any RNA structure including pseudoknot structures (pk-structure). We represent pk-structures...
  • KNOTTIN

  • Referenced in 2 articles [sw26871]
  • their structure, which form a unique pseudoknot. Since 2004, the KNOTTIN database (www.dsimb.inserm.fr/KNOTTIN/)...
  • DAFS

  • Referenced in 1 article [sw17125]
  • updated. Furthermore, we extend DAFS to consider pseudoknots in RNA structural alignments by integrating IPknot ... predicting a pseudoknotted structure. The experiments on publicly available datasets showed that DAFS can produce...
  • MINT

  • Referenced in 1 article [sw16407]
  • structure motifs (helices, junctions, loops, etc.) and pseudoknots. MINT also estimates the energy of stacking...
  • RNA2D3D

  • Referenced in 1 article [sw17141]
  • structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing...
  • CARNA

  • Referenced in 1 article [sw23122]
  • structures, but is able to align arbitrary pseudoknots...
  • peppercorn

  • Referenced in 1 article [sw33638]
  • reactions and products. Peppercorn supports arbitrary non-pseudoknotted structures and the following domain-level reactions...
  • Mathematica

  • Referenced in 5883 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Rfam

  • Referenced in 33 articles [sw04637]
  • The Rfam database is a collection of RNA...
  • OEIS

  • Referenced in 3387 articles [sw07248]
  • The On-Line Encyclopedia of Integer Sequence. The...
  • RNAshapes

  • Referenced in 7 articles [sw07960]
  • RNAshapes: an integrated RNA analysis package based on...
  • RNAsoft

  • Referenced in 7 articles [sw09073]
  • RNAsoft: a suite of RNA secondary structure prediction...
  • RNAfold

  • Referenced in 5 articles [sw10505]
  • RNAfold 2.1.8: Calculate minimum free energy secondary structures...
  • RNAsubopt

  • Referenced in 6 articles [sw10506]
  • RNAsubopt 2.1.8: calculate suboptimal secondary structures of RNAs...