Sooyoung Cha

The paper predicts quaternary structures of viral proteins using AlphaFold2 and AlphaFold-Multimer, identifying new insights into vaccinology and protease targets.

Reward-guided inference-time search over the Proteína-Complexa sequence-structure codesign model yields validated binders across 127 targets, kinases and a free carbohydrate, with codesigned sequences outperforming ProteinMPNN redesign.

Foldseek-Interface clusters protein interaction interfaces from PDB data, revealing 77,167 interface clusters and novel interface types.

The paper expands the AlphaFold Protein Structure Database to include proteome-scale quaternary structures, predicting 1.81M high-confidence protein complexes and revealing conserved structural clusters across domains of life.

StrucTTY provides real-time, interactive visualization of protein structures in text-only terminals using ASCII graphics and supports multi-structure comparison and Foldseek alignments.

The paper introduces GPU-accelerated homology search with MMseqs2, achieving faster sequence similarity detection than CPU methods and improving structure prediction speeds.

The paper uses 3D protein structures to evaluate human protein isoforms for biological functionality, refining genome annotations.