RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks
SE Butcher, AM Pyle - Accounts of chemical research, 2011 - ACS Publications
RNA molecules adopt specific three-dimensional structures critical to their function. Many
essential metabolic processes, including protein synthesis and RNA splicing, are carried out …
essential metabolic processes, including protein synthesis and RNA splicing, are carried out …
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
MJ Boniecki, G Lach, WK Dawson… - Nucleic acids …, 2016 - academic.oup.com
RNA molecules play fundamental roles in cellular processes. Their function and interactions
with other biomolecules are dependent on the ability to form complex three-dimensional …
with other biomolecules are dependent on the ability to form complex three-dimensional …
Automated de novo prediction of native-like RNA tertiary structures
RNA tertiary structure prediction has been based almost entirely on base-pairing constraints
derived from phylogenetic covariation analysis. We describe here a complementary …
derived from phylogenetic covariation analysis. We describe here a complementary …
The building blocks and motifs of RNA architecture
NB Leontis, A Lescoute, E Westhof - Current opinion in structural biology, 2006 - Elsevier
RNA motifs can be defined broadly as recurrent structural elements containing multiple
intramolecular RNA–RNA interactions, as observed in atomic-resolution RNA structures …
intramolecular RNA–RNA interactions, as observed in atomic-resolution RNA structures …
Crystal structure of a self-splicing group I intron with both exons
PL Adams, MR Stahley, AB Kosek, J Wang, SA Strobel - Nature, 2004 - nature.com
The discovery of the RNA self-splicing group I intron provided the first demonstration that not
all enzymes are proteins. Here we report the X-ray crystal structure (3.1-Å resolution) of a …
all enzymes are proteins. Here we report the X-ray crystal structure (3.1-Å resolution) of a …
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures
New methods are described for finding recurrent three-dimensional (3D) motifs in RNA
atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with …
atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with …
RNA structural motifs: building blocks of a modular biomolecule
DK Hendrix, SE Brenner, SR Holbrook - Quarterly reviews of …, 2005 - cambridge.org
1. Introduction 2222. What is an RNA motif? 2222.1 Sequence vs. structural motifs 2222.2
RNA structural motifs 2232.3 RNA structural elements vs. motifs 2232.4 Specific recognition …
RNA structural motifs 2232.3 RNA structural elements vs. motifs 2232.4 Specific recognition …
The ribosomal peptidyl transferase center: structure, function, evolution, inhibition
The ribosomal peptidyl transferase center (PTC) resides in the large ribosomal subunit and
catalyzes the two principal chemical reactions of protein synthesis: peptide bond formation …
catalyzes the two principal chemical reactions of protein synthesis: peptide bond formation …
RNA backbone is rotameric
LJW Murray, WB Arendall III… - Proceedings of the …, 2003 - National Acad Sciences
Despite the importance of local structural detail to a mechanistic understanding of RNA
catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to …
catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to …