A new entropy model for RNA: part IV, The Minimum Free Energy (mFE) and the thermodynamically most-probable folding pathway (TMPFP)
Explore this paper's citation graph
Summary
It is the supposition that some structures cannot be fit uniquely by the DPA, but may exist in real biology situations when disordered regions in the biomolecule are necessary, and this grants some qualitative tools to identify truly random RNA sequences.
- Type
- article
- Published
- 2015-07-13
- Cited by
- 1
- References
- 81
- Access
- Open access
- OpenAlex
- https://openalex.org/W1656490176
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:83576542
Keywords
Folding (DSP implementation), Degeneracy (biology), RNA, Computer science, Entropy (arrow of time)
References
- Globin mRNA sequences: analysis of base pairing and evolutionary implications.
- Computing folding pathways between RNA secondary structures
- Detecting pseudoknots and other local base-pairing structures in RNA sequences.
- DP Algorithms for RNA Secondary Structure Prediction with Pseudoknots
- Staphylococcal nuclease: a showcase of m-value effects.
- Free energy of imperfect nucleic acid helices. II. Small hairpin loops.
- Principles of Polymer Chemistry
- SPA: Short peptide analyzer of intrinsic disorder status of short peptides
- Fast folding and comparison of RNA secondary structures
- Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
- Molecular model for 5-S RNA. A small-angle x-ray scattering study of native, denatured and aggregated 5-S RNA from Escherichia coli ribosomes.
- Helix formation by d(TA) oligomers. II. Analysis of the helix-coli transitions of linear and circular oligomers.
- How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
- Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.
- Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides.
- Compact and ordered collapse of randomly generated RNA sequences
- RNA folding during transcription.
- Self-complementary oligoribonucleotides: effects of helix defects and guanylic acid-cytidylic acid base pairs.
- How RNA folds.
- Encoding folding paths of RNA switches
Cited by
Related papers
- THE DEGENERACY PROBLEM OF TWO-DIMENSIONAL LINEAR RECURRING ARRAYS
- A weak degeneracy revealing decomposition for the CANDECOMP/PARAFAC model
- Quantum Degeneracy in Two Dimensional Systems
- Degeneracy in the particle-in-a-box problem
- Considerations for predicting freezeout and exhaustion under a variety of nontrivial conditions
- Considerations for predicting freezeout and exhaustion under a variety of nontrivial conditions
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops
- Structures of RNA repeats associated with neurological diseases
- e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features
- Structural Elements in RNA