A partition function algorithm for nucleic acid secondary structure including pseudoknots. Export

@article{citeulike:118685, abstract = {Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N(5)) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications.}, address = {Department of Chemistry, California Institute of Technology, Pasadena, California 91125, USA.}, author = {Dirks, R. M. and Pierce, N. A.}, citeulike-article-id = {118685}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.10296}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/12926009}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=12926009}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/104553730/ABSTRACT}, doi = {10.1002/jcc.10296}, issn = {0192-8651}, journal = {J Comput Chem}, keywords = {dirks}, month = {October}, number = {13}, pages = {1664--1677}, posted-at = {2009-01-17 03:15:20}, priority = {2}, title = {A partition function algorithm for nucleic acid secondary structure including pseudoknots.}, url = {http://dx.doi.org/10.1002/jcc.10296}, volume = {24}, year = {2003} }

TY - JOUR ID - citeulike:118685 L3 - citeulike-article-id:118685 N2 - Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N(5)) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications. IS - 13 JF - J Comput Chem SN - 0192-8651 AD - Department of Chemistry, California Institute of Technology, Pasadena, California 91125, USA. EP - 1677 TI - A partition function algorithm for nucleic acid secondary structure including pseudoknots. VL - 24 SP - 1664 KW - dirks AU - Dirks, RM AU - Pierce, NA PY - 2003/10// UR - http://dx.doi.org/10.1002/jcc.10296 ER -