Related papers: Fast and Versatile RNA Design via Motif-level Divi…

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…

RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…

RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to the exponentially large sequence space and exponentially many…

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of…

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…

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…

Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…

The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop…

We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…

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…

The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which can tremendously impact their cost and…

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains…

The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA…

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…

RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…

RNA inverse sequence design has broad biological and engineering applications, but computational methods for practical design queries remain limited. Such queries may impose several constraints at once, including target folds or motifs,…

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…

RNA 3D motifs are recurrent substructures, modelled as networks of base pair interactions, which are crucial for understanding structure-function relationships. The task of automatically identifying such motifs is computationally hard, and…

An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…

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…