Daniel B. Haack

De novo design of RNA pseudoknots with deep learning

This paper demonstrates that deep learning can accurately design RNA pseudoknots, achieving results comparable to human experts in a competition.

Cryo-EM of a nucleotide-polymerizing ribozyme enables its predictive improvement

The paper uses cryo-EM to study a ribozyme's structure, revealing how it evolved to polymerize nucleotides and how mutations can enhance its function.

Template-based RNA structure prediction advanced through a blind code competition

The paper describes a Kaggle competition for RNA 3D structure prediction, showing that template-based methods can outperform deep learning approaches.

Ensemble Refinement of mismodeled cryo-EM RNA Structures Using All-Atom Simulations

The paper refines cryo-EM RNA structures using all-atom simulations and metainference to account for structural flexibility, revealing inaccuracies in single-structure approaches.

Structural evidence for metal ion catalysis in the ribosome

The paper provides structural evidence for metal ion catalysis in peptide bond formation across ribosomes from bacteria, archaea, and eukaryotes.

Scaffold-enabled high-resolution cryo-EM structure determination of RNA

This paper presents a scaffold strategy to improve cryo-EM resolution for small RNAs, demonstrating high-resolution structures of a TPP riboswitch and its ligand binding dynamics.