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 …

Assessment of three‐dimensional RNA structure prediction in CASP15

R Das, RC Kretsch, AJ Simpkin… - Proteins: Structure …, 2023 - Wiley Online Library
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 …

Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction

Y Li, C Zhang, C Feng, R Pearce… - Nature …, 2023 - nature.com
RNAs are fundamental in living cells and perform critical functions determined by their
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 …

Assessment of protein–ligand complexes in CASP15

X Robin, G Studer, J Durairaj… - Proteins: Structure …, 2023 - Wiley Online Library
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 …

RNA target highlights in CASP15: Evaluation of predicted models by structure providers

RC Kretsch, ES Andersen, JM Bujnicki… - Proteins: Structure …, 2023 - Wiley Online Library
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 …

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 …

Current and future directions in network biology

M Zitnik, MM Li, A Wells, K Glass, DM Gysi… - arXiv preprint arXiv …, 2023 - arxiv.org
Network biology, an interdisciplinary field at the intersection of computational and biological
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

M Szikszai, M Magnus, S Sanghi, S Kadyan… - Journal of Molecular …, 2024 - Elsevier
With advances in protein structure prediction thanks to deep learning models like AlphaFold,
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 …