Related papers: Designing RNA Secondary Structures is Hard
Enumerative studies of RNA secondary structures were initiated four decades ago by Waterman and his coworkers. Since then, RNA secondary structures have been explored according to many different structural characteristics, for instance,…
An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations.…
We introduce a novel fully convolutional neural network (FCN) architecture for predicting the secondary structure of ribonucleic acid (RNA) molecules. Interpreting RNA structures as weighted graphs, we employ deep learning to estimate the…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
In this paper we study $k$-noncrossing, canonical RNA pseudoknot structures with minimum arc-length $\ge 4$. Let ${\sf T}_{k,\sigma}^{[4]} (n)$ denote the number of these structures. We derive exact enumeration results by computing the…
An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$…
In this paper we experiment with using neural network structures to predict a protein's secondary structure ({\alpha} helix positions) from only its primary structure (amino acid sequence). We implement a fully connected neural network…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the…
RNA plays a pivotal role in diverse biological processes, ranging from gene regulation to catalysis. Recent advances in RNA design, such as RfamGen, Ribodiffusion and RDesign, have demonstrated promising results, with successful designs of…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets…
Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative…
We propose a two-level stochastic context-free grammar (SCFG) architecture for parametrized stochastic modeling of a family of RNA sequences, including their secondary structure. A stochastic model of this type can be used for maximum a…
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…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…