The computer simulation of RNA folding pathways using a genetic algorithm. Export

@article{gen1, abstract = {A procedure for simulating the RNA folding process using the principles of genetic algorithm is proposed. The method allows one to simulate a folding pathway of RNA, including such processes as disruption of temporarily formed structures, the folding of a molecule during its synthesis and pseudoknot formation. The simulations are able to predict functional metastable foldings and kinetically driven transitions to more stable structures. The analysis of free energies for intermediate foldings allows estimation of the ranges of kinetic refolding barriers and suggests that in some RNAs the selective evolutionary pressure suppresses the possibilities for alternative structures that could form in the course of transcription. It is shown that the folding pathway simulation can result in structure predictions that are more consistent with phylogenetically proven structures than minimum energy solutions. This suggest that RNA folding kinetics is very important for the formation of functional RNA structures. Therefore, apart form its value for predictions of RNA structures, the proposed computer simulations can be a powerful tool in the studies of RNA folding features.}, address = {Institute of Theoretical Biology, Leiden University, The Netherlands.}, author = {Gultyaev, A. P. and van Batenburg, F. H. and Pleij, C. W.}, citeulike-article-id = {678841}, citeulike-linkout-0 = {http://dx.doi.org/10.1006/jmbi.1995.0356}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0022-2836(85)70356-7}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/7541471}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=7541471}, citeulike-linkout-4 = {http://www.sciencedirect.com/science/article/B6WK7-45S97FK-8S/2/27f2ae76b01d69123a39cc35eb6def16}, day = {30}, doi = {10.1006/jmbi.1995.0356}, issn = {0022-2836}, journal = {J Mol Biol}, keywords = {algorithm, genetic, rna, simulation}, month = {June}, number = {1}, pages = {37--51}, posted-at = {2008-03-26 20:57:30}, priority = {2}, title = {The computer simulation of RNA folding pathways using a genetic algorithm.}, url = {http://dx.doi.org/10.1006/jmbi.1995.0356}, volume = {250}, year = {1995} }

TY - JOUR ID - gen1 L3 - citeulike-article-id:678841 N2 - A procedure for simulating the RNA folding process using the principles of genetic algorithm is proposed. The method allows one to simulate a folding pathway of RNA, including such processes as disruption of temporarily formed structures, the folding of a molecule during its synthesis and pseudoknot formation. The simulations are able to predict functional metastable foldings and kinetically driven transitions to more stable structures. The analysis of free energies for intermediate foldings allows estimation of the ranges of kinetic refolding barriers and suggests that in some RNAs the selective evolutionary pressure suppresses the possibilities for alternative structures that could form in the course of transcription. It is shown that the folding pathway simulation can result in structure predictions that are more consistent with phylogenetically proven structures than minimum energy solutions. This suggest that RNA folding kinetics is very important for the formation of functional RNA structures. Therefore, apart form its value for predictions of RNA structures, the proposed computer simulations can be a powerful tool in the studies of RNA folding features. IS - 1 JF - J Mol Biol SN - 0022-2836 AD - Institute of Theoretical Biology, Leiden University, The Netherlands. EP - 51 TI - The computer simulation of RNA folding pathways using a genetic algorithm. VL - 250 SP - 37 KW - algorithm KW - genetic KW - rna KW - simulation AU - Gultyaev, AP AU - van Batenburg, FH AU - Pleij, CW PY - 1995/06/30/ UR - http://dx.doi.org/10.1006/jmbi.1995.0356 ER -