targetdiff

Diffusion-based molecular docking achieving SOTA blind docking performance, treating ligand pose prediction as generative diffusion over SE(3), with DiffDock-L update for improved generalization (MIT CSAIL, ICLR 2023)

Large-scale biomolecular instruction dataset for chemistry/biology LLMs (ICLR2024)

General multimodal protein design framework enabling DNA-encoding of chemistry for programmable enzyme design and diverse protein generation through diffusion-based generative modeling (190+ stars, Apache 2.0, 2026)

Learning the language of protein-protein interactions

LLM-based molecular optimization tool

Rectified Quaternion Flow for efficient protein backbone generation, 37× faster than RFDiffusion with 0.972 designability (ICML 2025)