Related papers: FRET-guided selection of RNA 3D structures
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…
One of the hallmarks of cancer cells is their exceptional ability to migrate within the extracellular matrix (ECM) for gaining access to the circulatory system, a critical step of cancer metastasis. RhoA, a small GTPase, is known to be a…
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base…
Predicting the 3D structure of a macromolecule, such as a protein or an RNA molecule, is ranked top among the most difficult and attractive problems in bioinformatics and computational biology. Its importance comes from the relationship…
Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
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…
This study presents a novel, versatile traction force microscopy framework for quantifying three-dimensional (3D) interfacial forces during bio-adhesion by integrating in situ stereo digital image correlation with finite element (FE)…
Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…
The reliability of machine learning in multiscale physical systems depends on how physical structure is embedded into the learning process. We investigate this in the context of turbulent multiphase flows, focusing on the prediction of…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
Motivation: Protein folding is a dynamic process during which a protein's amino acid sequence undergoes a series of 3-dimensional (3D) conformational changes en route to reaching a native 3D structure; the resulting 3D structural…
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 has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction…
An experimental strategy has been developed specifically for the study of composition-dependent phase behavior in multi-component artificial membranes. The strategy is based on steady-state measurements of fluorescence resonance energy…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
Understanding the structures of biological macromolecules is highly important as they are closely associated with cellular functionalities. Comprehending the precise organization actin filaments is crucial because they form the dynamic…
Soft materials often display complex behaviors that transition through apparent solid- and fluid-like regimes. While a growing number of microscale simulation methods exist for these materials, reduced-order models that encapsulate the…
Single-molecule F\"{o}rster resonance energy transfer (smFRET) has become a mainstream technique for probing biomolecular structural dynamics. The rapid and wide adoption of the technique by an ever-increasing number of groups has generated…