Boris Rudolfs

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.

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.

Redesigning the Eterna100 RNA design benchmark for the Vienna 2 folding engine

The paper updates the Eterna100 RNA design benchmark to work with ViennaRNA 2 and shows that design performance depends on the folding engine used.