Niksa Praljak

This paper introduces BioM3, a framework that uses natural language prompts to design functional proteins, achieving state-of-the-art performance in prediction and generating proteins with native-like structures and function.

This paper introduces ProtWave-VAE, a generative model combining VAE and autoregressive methods for protein design, showing it can infer functional patterns and generate synthetic proteins with experimental validation.

This study uses deep generative models to design synthetic SH3 domains functional in yeast stress signaling, showing a VAE can recapitulate natural function and classify orthologs by phylogeny and function.