Related papers: RNA structure prediction: progress and perspective
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…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
Given usefulness of protein language models (LMs) in structure and functional inference, RNA LMs have received increased attentions in the last few years. However, these RNA models are often not compared against the same standard. Here, we…
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…
Biomedical research has revealed the crucial role of miRNAs in the progression of many diseases, and computational prediction methods are increasingly proposed for assisting biological experiments to verify miRNA-disease associations…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs or catalytic sites. Here we explore methods to generate template libraries and algorithms to query…
Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Experimental results on hadronic structures are discussed in view of our physics understanding. Achievements and challenges are noted.
Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
The subcellular localization of RNAs, including long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), microRNAs (miRNAs) and other smaller RNAs, plays a critical role in determining their biological functions. For instance, lncRNAs are…
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…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…