RNA secondary structure design.

@article{Burghardt2007RNASS,
  title={RNA secondary structure design.},
  author={Bernd Burghardt and Alexander K. Hartmann},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  year={2007},
  volume={75 2 Pt 1},
  pages={
          021920
        }
}
  • B. Burghardt, A. Hartmann
  • Published 15 September 2006
  • Computer Science
  • Physical review. E, Statistical, nonlinear, and soft matter physics
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… 

Figures and Tables from this paper

Computational design of RNAs with complex energy landscapes
TLDR
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
TLDR
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
TLDR
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
TLDR
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.
TLDR
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.
Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering.
TLDR
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
TLDR
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
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
  • D. C. Dai, K. Wiese
  • Computer Science
    2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
  • 2009
TLDR
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.
Algorithmic complexity in computational biology: basics, challenges and limitations
TLDR
The aim of this review is to survey the main algorithmic solutions to intractable problems in computational biology, highlighting the importance of High-Performance Computing in this area.
...
1
2
...

References

SHOWING 1-10 OF 53 REFERENCES
Annual Review of Biochemistry
TLDR
In his story of his visit to India, Prof. A. V. Hill has emphasized the need for biological research in particular in order to solve the many complex Indian problems.
"J."
however (for it was the literal soul of the life of the Redeemer, John xv. io), is the peculiar token of fellowship with the Redeemer. That love to God (what is meant here is not God’s love to men)
“Bioinformatics” 특집을 내면서
TLDR
Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Discrete Applied Mathematics
TLDR
Significant progress has been made with solution of location problems and in preprocessing and decomposition for discrete optimization and on the application of techniques from combinational optimization to nonlinear problems.
Evol
  • 61, 114
  • 2005
Phys
  • Rev. E 71, 021913 (pages 9)
  • 2005
Whar- ton
  • J. Mol. Evol
  • 2005
Biol
  • 336, 607
  • 2004
J. Mol. Biol
  • J. Mol. Biol
  • 2004
Phys
  • Rev. E 69, 61912 (pages 10)
  • 2004
...
1
2
3
4
5
...