Related papers: Enumeration of RNA structures by Matrix Models
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
In this paper we study canonical $\gamma$-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $\gamma$-structure is composed by specific building…
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
In this paper we present a selfcontained analysis and description of the novel {\it ab initio} folding algorithm {\sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $\sigma$-canonical RNA structure. Here an RNA…
The branching of an RNA molecule is an important structural characteristic yet difficult to predict correctly, especially for longer sequences. Using plane trees as a combinatorial model for RNA folding, we consider the thermodynamic cost,…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
We present a numerical study of the ultrametric properties of the set of RNA secondary structures with the maximum number of base pairs (energetically degenerate minima) within the maximum matching model (Nussinov algorithm). Using 18…
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…