Related papers: Designing RNA Secondary Structures is Hard

The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…

Despite nearly two scores of research on RNA secondary structure and RNA-RNA interaction prediction, the accuracy of the state-of-the-art algorithms are still far from satisfactory. Researchers have proposed increasingly complex energy…

DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…

The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…

In this paper we introduce a novel, context-free grammar, {\it RNAFeatures$^*$}, capable of generating any RNA structure including pseudoknot structures (pk-structure). We represent pk-structures as orientable fatgraphs, which naturally…

RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…

Rising costs in recent years of developing new drugs and treatments have led to extensive research in optimization techniques in biomolecular design. Currently, the most widely used approach in biomolecular design is directed evolution,…

An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Hale\v{s} et al. in 2016, is to…

Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…

In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…

We give recurrence relations for the enumeration of symmetric elements within four classes of arc diagrams corresponding to certain involutions and set partitions whose blocks contain no consecutive integers. These arc diagrams are…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made…

In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum stack-length. We show that the numbers of $k$-noncrossing structures without isolated base pairs are significantly smaller than the number of all…

In this paper we analyze the length-spectrum of blocks in $\gamma$-structures. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time RNA folding. A $\gamma$-structure is…

We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…

The Ribonucleic Acid (RNA) inverse folding problem, designing nucleotide sequences that fold into specific tertiary structures, is a fundamental computational biology problem with important applications in synthetic biology and…

We further develop the large $ N $ formalism presented by some of us in earlier works in order to recursively calculate the partition function of a singly pseudoknotted RNA. We demonstrate that this calculation takes time proportional to…

Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…