Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Export

@article{mc, abstract = {A computer program is presented which determines the secondary structure of linear RNA molecules by simulating a hypothetical process of folding. This process implies the concept of 'nucleation centres', regions in RNA which locally trigger the folding. During the simulation, the RNA is allowed to fold into pseudoknotted structures, unlike all other programs predicting RNA secondary structure. The simulation uses published, experimentally determined free energy values for nearest neighbour base pair stackings and loop regions, except for new extrapolated values for loops larger than seven nucleotides. The free energy value for a loop arising from pseudoknot formation is set to a single, estimated value of 4.2 kcal/mole. Especially in the case of long RNA sequences, our program appears superior to other secondary structure predicting programs described so far, as tests on tRNAs, the LSU intron of Tetrahymena thermophila and a number of plant viral RNAs show. In addition, pseudoknotted structures are often predicted successfully. The program is written in mainframe APL and is adapted to run on IBM compatible PCs, Atari ST and Macintosh personal computers. On an 8 MHz 8088 standard PC without coprocessor, using STSC APL, it folds a sequence of 700 nucleotides in one and a half hour.}, address = {Department of Biochemistry, Gorlaeus Laboratories, University of Leiden, The Netherlands.}, author = {Abrahams, J. P. and van den Berg, M. and van Batenburg, E. and Pleij, C.}, citeulike-article-id = {678837}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/18.10.3035}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/18/10/3035}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/1693421}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=1693421}, day = {25}, doi = {10.1093/nar/18.10.3035}, issn = {0305-1048}, journal = {Nucleic Acids Res}, keywords = {carlo, folding, monte, rna, simulation}, month = {May}, number = {10}, pages = {3035--3044}, posted-at = {2008-03-26 20:55:33}, priority = {2}, title = {Prediction of RNA secondary structure, including pseudoknotting, by computer simulation.}, url = {http://dx.doi.org/10.1093/nar/18.10.3035}, volume = {18}, year = {1990} }

TY - JOUR ID - mc L3 - citeulike-article-id:678837 N2 - A computer program is presented which determines the secondary structure of linear RNA molecules by simulating a hypothetical process of folding. This process implies the concept of 'nucleation centres', regions in RNA which locally trigger the folding. During the simulation, the RNA is allowed to fold into pseudoknotted structures, unlike all other programs predicting RNA secondary structure. The simulation uses published, experimentally determined free energy values for nearest neighbour base pair stackings and loop regions, except for new extrapolated values for loops larger than seven nucleotides. The free energy value for a loop arising from pseudoknot formation is set to a single, estimated value of 4.2 kcal/mole. Especially in the case of long RNA sequences, our program appears superior to other secondary structure predicting programs described so far, as tests on tRNAs, the LSU intron of Tetrahymena thermophila and a number of plant viral RNAs show. In addition, pseudoknotted structures are often predicted successfully. The program is written in mainframe APL and is adapted to run on IBM compatible PCs, Atari ST and Macintosh personal computers. On an 8 MHz 8088 standard PC without coprocessor, using STSC APL, it folds a sequence of 700 nucleotides in one and a half hour. IS - 10 JF - Nucleic Acids Res SN - 0305-1048 AD - Department of Biochemistry, Gorlaeus Laboratories, University of Leiden, The Netherlands. EP - 3044 TI - Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. VL - 18 SP - 3035 KW - carlo KW - folding KW - monte KW - rna KW - simulation AU - Abrahams, JP AU - van den Berg, M AU - van Batenburg, E AU - Pleij, C PY - 1990/05/25/ UR - http://dx.doi.org/10.1093/nar/18.10.3035 ER -