Topological Classification of RNA Structures via Intersection Graph
- Computer Science, MathematicsTPNC
An abstract algebraic representation of RNA secondary structures as a composition of hairpins, considered as basic loops, and a novel methodology to classify RNA structures based on two topological invariants, the genus and the crossing number are proposed.
On Topological RNA Interaction Structures
- MathematicsJ. Comput. Biol.
The theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures and the generating function is algebraic, which implies that the numbers of interaction structures can be computed recursively.
On RNA-RNA interaction structures of fixed topological genus.
- MathematicsMathematical biosciences
New models and algorithms for RNA pseudoknot order assignment
- Computer Science
A novel graph coloring-based model for the problem of pseudoknot order assignment is introduced and a specialized heuristic operating on the proposed model and an alternative integer programming algorithm are shown that are compared with that of state-of-the-art algorithms.
Statistics of topological RNA structures
- MathematicsJournal of mathematical biology
A new bivariate generating function is derived whose singular expansion allows for analysis of the distributions of arcs, stacks, hairpin- , interior- and multi-loops and H-type pseudoknots, kissing hairpins and their respective expectation values.
Conformational Features of Topologically Classified RNA Secondary Structures
- BiologyPloS one
Results from topological classification suggest that complex pseudoknots are usually some well-known motifs that are themselves complex or the interaction results of some special motifs, even if the required thermodynamic parameters are currently unknown.
Topology and prediction of RNA pseudoknots
Gfold admits a topology-dependent parametrization of pseudoknot penalties that increases the sensitivity and positive predictive value of predicted base pairs by 10-20% compared with earlier approaches.
Genus trace reveals the topological complexity and domain structure of biomolecules
- BiologyScientific Reports
The genus trace turns out to be a useful and versatile tool, with many potential applications, and gives a way to quantify how much more complicated a biomolecule is than its nested secondary structure alone would indicate.
Persistent Homology Analysis of RNA
- Computer Science
The application of persistent homology, a topological data analysis tool, is introduced for computing persistent features (loops) of the RNA folding space to discover persistent structural features, which are the set of smallest components to which the RNA fold space can be reduced.
SHOWING 1-10 OF 59 REFERENCES
Enumeration of RNA structures by matrix models.
- MathematicsPhysical review letters
Using a recently proposed matrix model formulation for the RNA folding problem, exact results are obtained for the simple case of an RNA molecule with an infinitely flexible backbone, in which any arbitrary pair of bases is allowed.
How RNA folds.
- BiologyJournal of molecular biology
A folding algorithm to predict the structure of an RNA from its sequence is suggested, but to solve the RNA folding problem one needs thermodynamic data on tertiary structure interactions, and identification and characterization of metal-ion binding sites.
Predicting RNA pseudoknot folding thermodynamics
- Chemistry, BiologyNucleic acids research
A folding thermodynamics model is developed that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics and predicts strong sequence-dependent helix-loop competitions in the Pseudoknot stability and the resultant conformational switches between different hairpin and pseudok not structures.
Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
- BiologyProceedings of the National Academy of Sciences of the United States of America
It is reported that many pseudoknots can be predicted through long-time-scale RNA-folding simulations, which follow the stochastic closing and opening of individual RNA helices.
Pseudoknots in RNA Secondary Structures: Representation, Enumeration, and Prevalence
- BiologyJ. Comput. Biol.
A way to decompose and represent general secondary structures which extends the tree representation of the stem-loop structure is presented, and this is used to analyze the frequency of pseudoknots in known and in random secondary structures.
CATH--a hierarchic classification of protein domain structures.
NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA.
- Chemistry, BiologyScience
The solution structure of the pseudoknotted T arm and acceptor arm of the transfer RNA-like structure of turnip yellow mosaic virus (TYMV) was determined by nuclear magnetic resonance (NMR) spectroscopy.
A dynamic programming algorithm for RNA structure prediction including pseudoknots.
- Computer ScienceJournal of molecular biology
This is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model and a useful graphical representation borrowed from quantum field theory is adopted.