Grigory I. Nikolaev

SQUARNA improves RNA secondary structure prediction by combining stem maximization with free energy minimization, outperforming existing methods including deep learning models.

ClaPNAC classifies nucleic acid-protein contacts in 3D structures using geometric features, distinguishing stacking, pseudo pairs, and phosphate/ribose interactions.

SQUARNA is an RNA secondary structure prediction method that uses a greedy stem formation model, performing competitively on single sequences and outperforming existing tools on sequence alignment inputs.