Results 61 to 70 of about 1,301,283 (332)
Predicting RNA-small molecule binding sites by 3D structure [PDF]
arXiv, 2023 The prediction of RNA-small molecule binding sites is crucial for the discovery of effective drugs. Various computational methods have been developed to address this challenge, using information about the structure and sequence of RNA. In this study, we introduce CplxCavity, a combination of a new algorithm and a machine learning model specifically ...
arxiv
FEBS Letters, EarlyView.The NlpC_P60 superfamily of peptidases is recognised by its key role in bacterial cell wall homeostasis. Recently, studies have also described the involvement of NlpC_P60‐like enzymes in bacterial competitive mechanisms and pathogenesis across several lineages.
Catharina dos Santos Silva +1 more
wiley +1 more source
Mapping RNA–RNA interactome and RNA structure in vivo by MARIO
Nature Communications, 2016 Current methods for mapping RNA-RNA interactions have to rely on an ‘anchor’ protein or RNA. Here, the authors report the MARIO (Mapping RNA interactome in vivo) technology that can massively reveal RNA-RNA interactions and RNA structure from unperturbed
Tri C. Nguyen +9 more
doaj +1 more source
Interplay between single-stranded binding proteins on RNA secondary structure [PDF]
Phys. Rev. E 88, 052707 (2013), 2013 RNA protein interactions control the fate of cellular RNAs and play an important role in gene regulation. An interdependency between such interactions allows for the implementation of logic functions in gene regulation. We investigate the interplay between RNA binding partners in the context of the statistical physics of RNA secondary structure, and ...
arxiv +1 more source
Structure of Eukaryotic RNA Polymerases
Annual Review of Biophysics, 2008 The eukaryotic RNA polymerases Pol I, Pol II, and Pol III are the central multiprotein machines that synthesize ribosomal, messenger, and transfer RNA, respectively. Here we provide a catalog of available structural information for these three enzymes. Most structural data have been accumulated for Pol II and its functional complexes.
Cramer, P. +18 more
openaire +5 more sources
Statistics of topological RNA structures [PDF]
Journal of Mathematical Biology, 2016 29 pages, 13 ...
Christian M. Reidys, Thomas J. X. Li
openaire +4 more sources
Making tau amyloid models in vitro: a crucial and underestimated challenge
FEBS Letters, EarlyView.This review highlights the challenges of producing in vitro amyloid assemblies of the tau protein. We review how accurately the existing protocols mimic tau deposits found in the brain of patients affected with tauopathies. We discuss the important properties that should be considered when forming amyloids and the benchmarks that should be used to ...
Julien Broc, Clara Piersson, Yann Fichou
wiley +1 more source
FEBS Letters, EarlyView.The S1025 peptide is the major antidote to the YrzI toxin, which we renamed here as SpyT (Small Peptide YrzI Toxin) and SpyA (Small Peptide YrzI Antitoxin) (1). Degradation of the toxin–antitoxin spyTA mRNA, either by a translation‐dependent cleavage by the endoribonuclease Rae1 (2) or by direct attack by 3′‐exoribonucleases (3), also contributes to ...
Laetitia Gilet +4 more
wiley +1 more source
Improved RNA pseudoknots prediction and classification using a new topological invariant [PDF]
Phys. Rev. E 94, 042410 (2016), 2016 We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both I) the topological genus of the graph and II) the number of crossing arcs of the corresponding primitive graph. We
arxiv +1 more source
Characteristics and Prediction of RNA Structure [PDF]
BioMed Research International, 2014 RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is NP-hard. Most RNAs fold during transcription from DNA into RNA through a hierarchical pathway wherein secondary structures form prior to tertiary structures.
Daming Zhu +4 more
openaire +3 more sources