AI4Protein

De novo peptide design

Release Date	Name	Reference	Repository	Model Type	Experimental Validation	Notes
2022-05-10	TERMs	Protein Science 31.6 (2022): e4322	N/A	Scaffold-based	No
2022-05-24	Rifdock	Nature 605.7910 (2022): 551	Github	RifDock + RifGen	Yes	David Baker
2022-07-21	RFdesign	Science 377.6604 (2022): 387	Github	Hallucination + Inpainting	Yes	David Baker
2023-02-26	AfCycDesign	BioRxiv (2023): 2023-02	Github	AF2-based	Yes	Cyclic Peptide
2023-05-26	dl-binder-design	Nat. Commun 14.1 (2023): 2625	Github	Hallucination + Inpainting	Yes	David Baker, Benchmark
2023-06-28	PepPrCLIP	BioRxiv (2023): 2023-06	GithubN/A	ESM2 + Diffusion	Yes
2023-08-08	Evoplay	Nat. Mach. Intell 5.8 (2023): 845	Github	RL-based	Yes
2023-08-26	AfDesign	IJMS 24.17 (2023): 13257	Code1, Code2	AF2-based	No	Cyclic Peptide
2023-09-24	EvoPro	PNAS 120.49 (2023): e2307371120	Github	AF2 + ProteinMPNN	Yes
2023-10-05	PepMLM	ArXiv:2310.03842	Github	ESM2-based	Yes
2023-10-23	ColabFold + BO	GenBio@NeurIPS2023 Poster	N/A	ColabFold and BO	No	Bayesian Optimization
2023-10-25	EvoBind	Commun. Chem 6.1 (2023): 229	Gitlab	Foldseek + ESM-IF1	Yes
2024-03-08	PPFlow	BioRxiv (2024): 2024-03	N/A	Flow-based	No	PPBench2024
2024-02-21	PepGLAD	ArXiv:2402.13555	N/A	Diffusion-based	No
2024-03-06	AMP-Diffusion	BioRxiv (2024): 2024-03	N/A	ESM2 + Diffusion	No

Release Date	Model Name	Reference	Repository	Model Type	Tasks Type
2024-02-10	Scaffold-Lab	BioRxiv (2024): 2024-02	Github		Benchmark
2022-07-21	RFdesign	Science 377.6604 (2022): 387	Github	AF2-based	Hallucination, Unconditional, Inpainting
2022-06-27	Ig-VAE	PLoS Comput. Biol 18.6 (2022): e1010271	Github	VAE-based	Unconditional
2022-07-01	ProteinSGM	Nat. Comput. Sci 3.5 (2023): 382	Gitlab	Diffusion-based	Unconditional, Inpainting
2023-01-01	DiffSDS	ArXiv:2301.09642	Github	Diffusion-based	Inpainting
2023-01-29	Genie	ArXiv:2301.12485	Github	Diffusion-based	Unconditional
2023-02-05	FrameDiff	ArXiv:2302.02277	Github	Diffusion-based	Unconditional
2023-05-10	Protein Generator	BioRxiv (2023): 2023-05	Github Huggingface	Diffusion-based	Unconditional, Inpainting
2023-05-25	Protpardelle	BioRxiv (2023): 2023-05	Github	Diffusion-based	Unconditional, Side-chain conditional
2023-06-11	RFdiffusion	Nature 620.7976 (2023): 1089	Github	Diffusion-based	General
2023-06-30	TDS	ArXiv:2306.17775	Github	Diffusion-based	Conditional
2023-10-30	GPDL	BioRxiv (2023): 2023-10	Github	ESM-based	Conditional
2023-10-08	FrameFlow	ArXiv:2310.05297	Github	Flow-based	Unconditional
2023-11-15	Chroma	Nature 623.7989 (2023): 1070	Github	Diffusion-based	General
2024–02-28	PocketGen	BioRxiv (2024) 2024-02	Github	Bilevel graph transformer	Inpainting
2024–03-07	RFdiffusion-AA	Science (2024): eadl2528	Github	Diffusion-based	General

Name	Source Type	Affinity Type	Dataset Size	Protein Type	Download Link	Notes
SKEMPI 2.0	Dataset	ΔΔG/ΔG	6193/346	General	Link
ATLAS	Dataset	ΔΔG/ΔG	604/65	MHC-TCR	Link
GeoPPI	Paper	ΔΔG	6538	General	Link
mmCSM-PPI	Paper	ΔΔG	1340	General	Link	SKEMPI 2.0 + etc.
TopNetTree	Paper	ΔΔG	1290	Antigen-Antibody	Link	AB_Bind + etc.
AB_Bind	Dataset	ΔΔG	1101	Antigen-Antibody	Link
BindPPI	Paper	ΔG	1467	General	Link
NERE	Paper	ΔG	566	Antigen-Antibody	Link	From Sabdab
Sabdab	Dataset	ΔG	467	Antigen-Antibody	Link
CSM-AB	Paper	ΔG	473	Antigen-Antibody	Link	From Sabdab
AREA-AFFINITY	Paper	ΔG	297	Antigen-Antibody	Link	From CSM-ABB
LISA	Paper	ΔG	179	General	Link
PRO_580	Paper	ΔG	144	General	Link
Prodigy	Paper	ΔG	81	General	Link