[HTML][HTML] Toward a mechanistic understanding of DNA methylation readout by transcription factors
Epigenetic DNA modification impacts gene expression, but the underlying molecular
mechanisms are only partly understood. Adding a methyl group to a cytosine base locally …
mechanisms are only partly understood. Adding a methyl group to a cytosine base locally …
When will RNA get its AlphaFold moment?
The protein structure prediction problem has been solved for many types of proteins by
AlphaFold. Recently, there has been considerable excitement to build off the success of …
AlphaFold. Recently, there has been considerable excitement to build off the success of …
RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning
The majority of our human genome transcribes into noncoding RNAs with unknown
structures and functions. Obtaining functional clues for noncoding RNAs requires accurate …
structures and functions. Obtaining functional clues for noncoding RNAs requires accurate …
RIC-seq for global in situ profiling of RNA–RNA spatial interactions
Z Cai, C Cao, L Ji, R Ye, D Wang, C Xia, S Wang, Z Du… - Nature, 2020 - nature.com
Highly structured RNA molecules usually interact with each other, and associate with
various RNA-binding proteins, to regulate critical biological processes. However, RNA …
various RNA-binding proteins, to regulate critical biological processes. However, RNA …
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
Abstract Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used
w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing …
w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing …
Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance
T Ohira, K Minowa, K Sugiyama, S Yamashita… - Nature, 2022 - nature.com
Post-transcriptional modifications have critical roles in tRNA stability and function,,–. In
thermophiles, tRNAs are heavily modified to maintain their thermal stability under extreme …
thermophiles, tRNAs are heavily modified to maintain their thermal stability under extreme …
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction
RNAs are fundamental in living cells and perform critical functions determined by their
tertiary architectures. However, accurate modeling of 3D RNA structure remains a …
tertiary architectures. However, accurate modeling of 3D RNA structure remains a …
RNA force field with accuracy comparable to state-of-the-art protein force fields
Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an
atomic level of detail the conformational changes undergone by proteins. The application of …
atomic level of detail the conformational changes undergone by proteins. The application of …
Structures of small molecules bound to RNA repeat expansions that cause Huntington's disease-like 2 and myotonic dystrophy type 1
JL Chen, A Taghavi, AJ Frank, MA Fountain… - Bioorganic & medicinal …, 2024 - Elsevier
Trinucleotide repeat expansions fold into long, stable hairpins and cause a variety of
incurable RNA gain-of-function diseases such as Huntington's disease, the myotonic …
incurable RNA gain-of-function diseases such as Huntington's disease, the myotonic …
Multiple sequence alignment-based RNA language model and its application to structural inference
Compared with proteins, DNA and RNA are more difficult languages to interpret because
four-letter coded DNA/RNA sequences have less information content than 20-letter coded …
four-letter coded DNA/RNA sequences have less information content than 20-letter coded …