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The shape that organic molecules such as biopolymers form within organic systems largely determines the function said molecules perform. RNA is a biopolymer that plays a central part in several stages of protein synthesis, and also has structural, functional, and regulatory roles in the cell. In an ab initio case most common structure prediction techniques employ minimization of the free energy of...
Pseudoknots are RNA tertiary structures which perform essential biological functions. This paper presents SARNA-Predict-pk, an algorithm for pseudoknotted RNA secondary structure prediction based on Simulated Annealing (SA). The research presented here extends previous work of SARNA-Predict and incorporates a new thermodynamic model into the algorithm, effectively enabling it to predict pseudo-knotted...
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