When will RNA get its AlphaFold moment?
B Schneider, BA Sweeney, A Bateman… - Nucleic Acids …, 2023 - academic.oup.com
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 …
Assessment of three‐dimensional RNA structure prediction in CASP15
The prediction of RNA three‐dimensional structures remains an unsolved problem. Here, we
report assessments of RNA structure predictions in CASP15, the first CASP exercise that …
report assessments of RNA structure predictions in CASP15, the first CASP exercise that …
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 …
The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15
B Ozden, A Kryshtafovych… - … : Structure, Function, and …, 2023 - Wiley Online Library
In CASP15, 87 predictors submitted around 11 000 models on 41 assembly targets. The
community demonstrated exceptional performance in overall fold and interface contact …
community demonstrated exceptional performance in overall fold and interface contact …
Assessment of protein–ligand complexes in CASP15
CASP15 introduced a new category, ligand prediction, where participants were provided
with a protein or nucleic acid sequence, SMILES line notation, and stoichiometry for ligands …
with a protein or nucleic acid sequence, SMILES line notation, and stoichiometry for ligands …
RNA target highlights in CASP15: Evaluation of predicted models by structure providers
The first RNA category of the Critical Assessment of Techniques for Structure Prediction
competition was only made possible because of the scientists who provided experimental …
competition was only made possible because of the scientists who provided experimental …
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15
A Kryshtafovych, GT Montelione… - Proteins: Structure …, 2023 - Wiley Online Library
For the first time, the 2022 CASP (Critical Assessment of Structure Prediction) community
experiment included a section on computing multiple conformations for protein and RNA …
experiment included a section on computing multiple conformations for protein and RNA …
Current and future directions in network biology
Network biology, an interdisciplinary field at the intersection of computational and biological
sciences, is critical for deepening understanding of cellular functioning and disease. While …
sciences, is critical for deepening understanding of cellular functioning and disease. While …
[HTML][HTML] RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction
With advances in protein structure prediction thanks to deep learning models like AlphaFold,
RNA structure prediction has recently received increased attention from deep learning …
RNA structure prediction has recently received increased attention from deep learning …
RNAhugs web server for customized 3D RNA structure alignment
M Zurkowski, M Swiercz, F Wozny… - Nucleic Acids …, 2024 - academic.oup.com
Alignment of 3D molecular structures involves overlaying their sets of atoms in space in such
a way as to minimize the distance between the corresponding atoms. The purpose of this …
a way as to minimize the distance between the corresponding atoms. The purpose of this …