Related papers: FRET-guided selection of RNA 3D structures
Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
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…
Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized,…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
We present FLOWR.root, an SE(3)-equivariant flow-matching model for pocket-aware 3D ligand generation with joint potency and binding affinity prediction and confidence estimation. The model supports de novo generation, interaction- and…
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…
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…
In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP). Output from MaP provides information about both pairing (via reactivities) and contact…
Recent genome and transcriptome sequencing projects have unveiled a plethora of highly structured RNA molecules as central mediators of cellular function. Single molecule Forster Resonance Energy Transfer (smFRET) is a powerful tool for…
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D…