A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.

ABSTRACT: The accurate prediction of RNA secondary structure from primary sequence has had enormous impact on research from the past 40 years. Although many algorithms are available to make these predictions, the inclusion of non-nested loops, termed pseudoknots, still poses challenges arising from two main factors: 1) no physical model exists to estimate the loop entropies of complex intramolecular pseudoknots, and 2) their NP-complete enumeration has impeded their study. Here, we address both challenges. First, we develop a polymer physics model that can address arbitrarily complex pseudoknots using only two parameters corresponding to concrete physical quantities-over an order of magnitude fewer than the sparsest state-of-the-art phenomenological methods. Second, by coupling this model to exhaust

SUBMITTER: Kimchi O 

PROVIDER: S-EPMC6697467 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature