Marta Szachniuk

RNApdbee 3.0: A unified web server for comprehensive RNA secondary structure annotation from 3D coordinates

RNApdbee 3.0 provides a unified web server for RNA secondary structure annotation using 3D coordinates, integrating 2D and 3D data and standardizing inputs to PDBx/mmCIF.

Machine learning-guided design of artificial microRNAs for targeted gene silencing

The paper introduces miRarchitect, a machine learning platform for designing artificial microRNAs, showing it produces functional amiRNAs more effectively than existing tools.

RNAtive to recognize native-like structure in a set of RNA 3D models

RNAtive evaluates RNA 3D models using consensus secondary structures without experimental references, identifying native-like folds in computational predictions.

Knotted artifacts in predicted 3D RNA structures

The paper analyzes 3D RNA structure prediction models from CASP15 and finds that all entanglements are artifacts, with ML methods more prone to generating them than traditional methods.

Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions

The paper reports RNA 3D structure prediction results for SARS-CoV-2 5'- and 3'-UTRs using computational methods and expert analysis.

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

The paper evaluates the stereochemical quality of RNA 3D models from RNA-Puzzles submissions and identifies deviations from standard RNA stereochemistry.