Stochastic Local Search: Foundations & Applications
Stochastic Local Search: Foundations & Applications
Structure clustering features on the Sfold Web server
Bioinformatics
INFO-RNA---a fast approach to inverse RNA folding
Bioinformatics
RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inverting the Viterbi algorithm: an abstract framework for structure design
Proceedings of the 25th international conference on Machine learning
RNA-DV: an interactive tool for editing and visualizing RNA secondary structures
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Flexible RNA design under structure and sequence constraints using formal languages
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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The RNA secondary structure design (SSD) problem is a recently emerging research topic motivated by applications such as customized drug design and the self-assembly of RNA nano-objects. This paper presents a novel local search algorithm, rnaDesign for SSD solving. An evaluation of the algorithm performance in terms of sequence affinity and structure specificity is made through comparison with another algorithm, RNAinverse. Experiments were performed on RNA secondary structures including three biologically existing data sets and one random structure set. Empirical results show that rnaDesign outperforms RNAinverse in terms of structure designability; sequences designed by rnaDesign also exhibit better thermodynamic stability with relatively lower folding energy. Furthermore, we demonstrate through parameter tuning experiments that using a combination of heuristic search strategies leads to better design performance; there also exists a strong correlation between the heuristic values in use and solution quality.