💡 Notes

The following lists are curated by humans, as such may be incomplete
We only include software targeting the inverse folding problem e.g given a structure predict the sequence that folds into it. This is also referred to as protein sequence design. Note, that most models here model P(sequence | structure).
We do not wish to advertize one tool over any other, but simply list the tools we are aware of in order of publication year of the model, preprint or publication (whichever is first)
Any suggestions for improvements and additions are welcome as issues or pull requests

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Protein Sequence Design / Inverse folding models

(sorted by year of release)

Name	Release year	Architecture	Paper	Code	Notes	Experimental validation
Wazy Alphafold	2022	Transformer	biorxiv	-	colab	-
ABACUS-R	2022	Transformer	Nat Comput Sci	code		✅
ProteinMPNN	2022	MPNN	biorxiv	git	webserver	✅
ProDESIGN-LE	2022	Transformer	biorxiv	-		-
RaSP	2022	3DCNN	biorxiv	git	colab	-
MIF	2022	SGNN	biorxiv	git		-
ESM-IF1	2022	Transformer	biorxiv	git		-
Partlon et al.	2022	Transformer	biorxiv	-		-
TIMED-*	2022	3DCNN	arxiv	git		not published yet
AF2rank (ColabDesign)	2022	AlphaFold	biorxiv	git		-
GCNDesign	2021	GCN	pdf	git	colab	-
GX	2021	3DCNN+GNN	arxiv	git		not published yet
Fold2Seq	2021	Transformer	arxiv	git		-
CNN_protein_landscape	2021	3DCNN	Journal of Biological Physics	git		-
Orellana et al.	2021	GVP	biorxiv	-		-
Jing et al.	2020	GVP	arxiv	git
DenseCPD	2020	3DCNN	JCIM	-	webserver	-
ProDCoNN	2020	3DCNN	Proteins	-		-
ProteinSolver	2020	GNN	Cell Systems	gitlab	webserver	✅
MutCompute	2020	3DCNN	ACS SynBio	-	webserver	✅
Ingraham et al.	2019	Transformer	NeurIPS Proceedings	git		-
3DCNN	2017	3DCNN	BMC Bioinformatics	-		-

Protein Sequence & Rotamer Design / Inverse folding models

(sorted by year of release)

Name	Release year	Architecture	Paper	Code	Notes	Experimental validation
TIMED_Rotamer	2022	3DCNN	-	git		not published yet
SeqDes	2021	3DCNN	Nature Comm - BioRxiv	git		✅