Table 2 |.

Open-source diffusion model tools for bioinformatics

Applications	Tool name	Denoising condition	Diffusion framework	Network architecture	Github
Protein design and generation	ProteinSGM91	Conditioned and unconditioned	Score SDE	Convolutional neural network	CODE
	FoldingDiff101	Unconditioned	DDPM	Transformer	CODE
	Genie103	Unconditioned	DDPM	Variant SE(3)-transformer	CODE
	SMCDiff104	Conditioned	Score SDE	EGNN	CODE
	FrameDiff106	Unconditioned	Score SDE	SE(3)-transformer	CODE
	RFdiffusion105	Conditioned and unconditioned	DDPM	SE(3)-transformer	CODE
	Chroma107	Conditioned	Score SDE	GNN	CODE
Small-molecule generation and drug design	EDM54	Conditioned	DDPM	EGNN	CODE
	SDEGen111	Conditioned	Score SDE	GNN	CODE
	DiffLinker113	Conditioned	DDPM	EGNN	CODE
Protein-ligand interaction modelling	DiffBP114	Conditioned	DDPM	EGNN	CODE
	DiffSBDD115	Conditioned	DDPM	EGNN	CODE
	DiffDock116	Conditioned	Score SDE	Variant EGNN	CODE
Cryo-EM data analysis	CryoDRGN98	Conditioned	Score SDE	VAE	CODE
Single-cell image and gene-expression data analysis	DISPR99	Conditioned	DDPM	U-Net	CODE

Score SDE, score stochastic differential equation; DDPM, denoising diffusion probabilistic model; EGNN, equivariant GNN; GNN, graph neural network; cryo-EM, cryogenic electron microscopy; VAE, variational autoencoder; U-Net, U-shaped neural network.