Results 81 to 90 of about 1,640,958 (330)
Fatgraph models of RNA structure
Computational and Mathematical Biophysics, 2017 In this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We discuss various notions of coarse-grained RNA structures and relate them to fatgraphs.We motivate and discuss the main intuition behind the fatgraph model and ...
Huang Fenix +2 more
doaj +1 more source
RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing
Genomics, Proteomics & Bioinformatics, 2017 RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA structuromes, have been developed. Applications of these approaches to
Meiling Piao +2 more
doaj +1 more source
Flexible RNA design under structure and sequence constraints using formal languages [PDF]
, 2013 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.
Denise, Alain +5 more
core +5 more sources
Shapes of RNA Pseudoknot Structures [PDF]
Journal of Computational Biology, 2010 24 pages, 7 figures,
Reidys, Christian M., Wang, Rita R.
openaire +3 more sources
Disordered but rhythmic—the role of intrinsic protein disorder in eukaryotic circadian timing
FEBS Letters, EarlyView.Unstructured domains known as intrinsically disordered regions (IDRs) are present in nearly every part of the eukaryotic core circadian oscillator. IDRs enable many diverse inter‐ and intramolecular interactions that support clock function. IDR conformations are highly tunable by post‐translational modifications and environmental conditions, which ...
Emery T. Usher, Jacqueline F. Pelham
wiley +1 more source
Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST
Nature CommunicationsThe fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits ...
Yufan Zhang +6 more
doaj +1 more source
RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database
BMC Bioinformatics, 2008 Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a ...
Andronescu Mirela +3 more
doaj +1 more source
RNA-RNA interaction prediction based on multiple sequence alignments
, 2010 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 interaction ...
Li, Andrew X. +3 more
core +1 more source
Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation
FEBS Letters, EarlyView.Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe +3 more
wiley +1 more source
The role of histone modifications in transcription regulation upon DNA damage
FEBS Letters, EarlyView.This review discusses the critical role of histone modifications in regulating gene expression during the DNA damage response (DDR). By modulating chromatin structure and recruiting repair factors, these post‐translational modifications fine‐tune transcriptional programmes to maintain genomic stability.
Angelina Job Kolady, Siyao Wang
wiley +1 more source