RNA folding including pseudoknots and "real knots"
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Related Publications
Isambert H: The jerky and knotty dynamics of RNA. Methods, 49(2):189-96 (2009). [review] Pubmed | ScienceDirect | pdf
Xayaphoummine A, Bucher T, Isambert H: Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res, 33:W605-10 (2005). Pubmed | OXFORD | pdf | supp | Kinefold server
Xayaphoummine A, Bucher T, Thalmann F, Isambert H: Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc Natl Acad Sci USA, 100(26):15310-5 (2003). Pubmed | PNAS | pdf
Isambert H, Siggia ED: Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc Natl Acad Sci USA, 97(12):6515-20 (2000). Pubmed | PNAS | pdf [featured by Science]