Related papers: FRET-guided selection of RNA 3D structures
3D fragment reassembly aims to recover the rigid poses of unordered fragment point clouds or meshes in a common object coordinate system to reconstruct the complete shape. The problem becomes particularly challenging as the number of…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
We propose a new deterministic methodology to predict RNA sequence and protein folding. Is stem enough for structure prediction? The main idea is to consider all possible stem formation in the given sequence. With the stem loop energy 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…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
Background: One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the sequence-structure relationship. Accurate…
Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
It is acknowledged that co-evolutionary nucleotide-nucleotide interactions are essential for RNA structures and functions. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequence from its homologous sequence…
Single-molecule F\"orster Resonance Energy Transfer (smFRET) is ideally suited to resolve the dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly…
Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field,…
Multicomponent lipid mixtures exhibit complex phase behavior, including coexistence of nanoscopic fluid phases in ternary mixtures mimicking the composition of the outer leaflet of mammalian plasma membrane. The physical mechanisms…
In post-transcriptional regulation, an mRNA molecule is bound by many proteins and/or miRNAs to modulate its function. To enable combinatorial gene regulation, these binding partners of an RNA must communicate with each other, exhibiting…