2004/05/19 by G. Vernizzi, Graziano Vernizzi, H. Orland +5
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Biomolecules (q-bio.BM) #Chemical Synthesis and Analysis #FOS: Biological sciences #FOS: Physical sciences #RNA and protein synthesis mechanisms #Soft Condensed Matter (cond-mat.soft) #Surface Chemistry and Catalysis #cond-mat.soft #q-bio.BM
paper · pdf · doi:10.48550/arxiv.q-bio/0405014
22 pages, 14 figures
arxiv created 2004/05/19 · openalex publication_date 2004/05/19 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the non-planar topologies of RNA structures and propose a classification of RNA pseudoknots according to the minimal genus of the surface on which the RNA structure can be embedded. This classification provides a simple and natural way to tackle the problem of RNA folding prediction in presence of pseudoknots. Based on that approach, we describe a Monte Carlo algorithm for the prediction of pseudoknots in an RNA molecule.