# RNA secondary structure design.

@article{Burghardt2006RNASS, title={RNA secondary structure design.}, author={Bernd Burghardt and Alexander K. Hartmann}, journal={Physical review. E, Statistical, nonlinear, and soft matter physics}, year={2006}, volume={75 2 Pt 1}, pages={ 021920 } }

We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure we want to find a sequence that has a certain structure as its ground state. If such a sequence exists, the structure is called designable. We have implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact answer as to whether such a sequence exists. The bounds required by the branch-and-bound algorithm…

## 12 Citations

### Computational design of RNAs with complex energy landscapes

- BiologyBiopolymers
- 2013

This work introduces a user‐friendly tool for designing RNA sequences that fold into multiple target structures and demonstrates that bi‐ and tri‐stable “switches” can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures.

### rnaDesign: Local search for RNA secondary structure design

- Computer Science2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
- 2009

A novel local search algorithm, rnaDesign for SSD solving, which demonstrates 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.

### Algorithms for Nucleic Acid Sequence Design

- Computer Science
- 2010

An algorithm for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium is described, and this algorithm is extended to design multi-state systems with an arbitrary number of linked targets and demonstrates its efficacy on systems invented by molecular engineers.

### Nucleic acid sequence design via efficient ensemble defect optimization

- Computer ScienceJ. Comput. Chem.
- 2011

An algorithm for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium is described and exhibits asymptotic optimality and the exponent in the time complexity bound is sharp.

### Sequence Design for a Test Tube of Interacting Nucleic Acid Strands.

- BiologyACS synthetic biology
- 2015

For target test tubes representative of design challenges in the molecular programming and synthetic biology communities, the test tube design algorithm typically succeeds in achieving a normalized test tube ensemble defect ≤1% at a design cost within an order of magnitude of the cost of test tube analysis.

### Fast free-energy-based neutral set size estimates for the RNA genotype–phenotype map

- BiologyJournal of the Royal Society Interface
- 2022

It is found that structures with high neutral sets in one framework also tend to have largeneutral sets in the other framework for a range of parameters and thus the choice of GP map does not fundamentally affect which structures have the largest neutral set sizes.

### Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering.

- BiologyJournal of the American Chemical Society
- 2017

A framework for designing the sequences of multiple nucleic acid strands intended to hybridize in solution via a prescribed reaction pathway as a multistate optimization problem using a set of target test tubes to represent reactant, intermediate, and product states of the system, as well as to model crosstalk between components.

### Neutral network sizes of biological RNA molecules can be computed and are not atypically small

- BiologyBMC Bioinformatics
- 2008

The biological RNA structures examined are more abundant than random structures, which indicates that their robustness and their ability to produce new phenotypic variants may also be high, and a generalized Monte Carlo approach is introduced that can measure neutral set sizes in larger spaces.

### Neutral Network Sizes of Biological RNA Molecules Can Be Computed and Are Atypically Large

- Art

SFI Working Papers contain accounts of scientific work of the author(s) and do not necessarily represent the views of the Santa Fe Institute. We accept papers intended for publication in…

### Performance prediction for RNA design using parametric and non-parametric regression models

- Computer Science2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
- 2009

Empirical results show the non-parametric methods used for algorithm performance prediction for the RNA Secondary Structure Design problem achieve a higher prediction accuracy on biologically existing data, where biological data exhibits a higher degree of local similarity among individual instances.

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