RNA folding pathways and kinetics using 2D energy landscapes
The authors introduce a novel algorithm for determining the 2D projection of the energy landscape, which has the potential to facilitate the identification of RNA folding pathways. The paper commences with a description of the role and importance of RNA folding pathways and introduces, in the preliminary section, the basic concepts used throughout the paper. The presentation of the algorithm starts with the detailed description of the polynomial interpolation using the fast Fourier transform, which includes the recursions for computing the polynomial \(Z_{i,j}(x)\), the actual polynomial interpolation and the complexity reduction achieved by the precomputation of powers of the complex roots of unity. This improvement leads to a reduction of runtime complexity from \(O(n^7)\) to \(O(n^5)\) and space complexity from \(O(n^4)\) to \(O(n^2)\). The authors also include a benchmarking between RNA2Dfold and FFTbor2D and a detailed description of the folding kinetics along the 2D energy grid.
- The statistical mechanics of kinetically‐controlled RNA folding pathways
- RNA folding kinetics using Monte Carlo and Gillespie algorithms
- Cooperativity along kinetic pathways in RNA folding
- Efficient computation of RNA folding dynamics
- Impact of the energy model on the complexity of RNA folding with pseudoknots
- RNA Secondary Structure Prediction Via Energy Density Minimization
- An IP algorithm for RNA folding trajectories
- A continuous analogue for RNA folding
- An action principle for biopolymer folding in vitro: A new perspective on the design of expeditiously-folded RNA molecules
- RNA folding kinetics using Monte Carlo and Gillespie algorithms
- Barrier heights between ground states in a model of RNA secondary structure
- Information generation and the loss of conformational entropy during RNA folding
- An IP algorithm for RNA folding trajectories
- Arrhenius lifetimes of RNA structures from free energy landscapes
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