Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.

@article{citeulike:150261, abstract = {Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here we report that many pseudoknots can be predicted through long-time-scale RNA-folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n2) clustering algorithm that computes time averages over a continuously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 105-fold for short, multistable molecules (<or=150 bases). We performed extensive folding statistics on random and natural RNA sequences and found that pseudoknots are distributed unevenly among RNA structures and account for up to 30\% of base pairs in G+C-rich RNA sequences (online RNA-folding kinetics server including pseudoknots: http://kinefold.u-strasbg.fr).}, address = {Laboratoire de Dynamique des Fluides Complexes, Centre National de la Recherche Scientifique-Universit\'{e} Louis Pasteur, Institut de Physique, 3 Rue de l'Universit\'{e}, 67000 Strasbourg, France.}, author = {Xayaphoummine, A. and Bucher, T. and Thalmann, F. and Isambert, H. }, citeulike-article-id = {150261}, doi = {10.1073/pnas.2536430100}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {kinefold, kinetics, modeling, pseudoknot, rna}, month = {December}, number = {26}, pages = {15310--15315}, posted-at = {2008-04-15 18:02:44}, priority = {0}, title = {Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.}, url = {http://dx.doi.org/10.1073/pnas.2536430100}, volume = {100}, year = {2003} }

TY - JOUR ID - citeulike:150261 L3 - citeulike-article-id:150261 TI - Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. JF - Proc Natl Acad Sci U S A VL - 100 IS - 26 SP - 15310 EP - 15315 AD - Laboratoire de Dynamique des Fluides Complexes, Centre National de la Recherche Scientifique-Université Louis Pasteur, Institut de Physique, 3 Rue de l'Université, 67000 Strasbourg, France. SN - 0027-8424 N2 - Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here we report that many pseudoknots can be predicted through long-time-scale RNA-folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n2) clustering algorithm that computes time averages over a continuously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 105-fold for short, multistable molecules (<or=150 bases). We performed extensive folding statistics on random and natural RNA sequences and found that pseudoknots are distributed unevenly among RNA structures and account for up to 30% of base pairs in G+C-rich RNA sequences (online RNA-folding kinetics server including pseudoknots: http://kinefold.u-strasbg.fr). KW - kinefold KW - kinetics KW - modeling KW - pseudoknot KW - rna AU - Xayaphoummine, A AU - Bucher, T AU - Thalmann, F AU - Isambert, H PY - 2003/12/23/ UR - http://dx.doi.org/10.1073/pnas.2536430100 ER -