Protein Structure Prediction ML Frameworks

Tools for predicting 3D protein structures and complexes from sequences, including AlphaFold variants and related deep learning architectures. Does NOT include protein design/generation, molecular docking, or property prediction without structural output.

There are 17 protein structure prediction frameworks tracked. 2 score above 50 (established tier). The highest-rated is mxfold/mxfold2 at 53/100 with 162 stars.

Get all 17 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=ml-frameworks&subcategory=protein-structure-prediction&limit=20"

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#	Framework	Score	Tier	Stars	Language
1	mxfold/mxfold2 MXfold2: RNA secondary structure prediction using deep learning with...	53	Established	162	Python
2	kyegomez/Open-AF3 Implementation of Alpha Fold 3 from the paper: "Accurate structure...	52	Established	802	Python
3	PaddlePaddle/PaddleHelix Bio-Computing Platform Featuring Large-Scale Representation Learning and...	46	Emerging	1,107	Python
4	mjendrusch/salad protein structure generation with sparse all-atom denoising models	45	Emerging	60	Python
5	dptech-corp/Uni-Fold An open-source platform for developing protein models beyond AlphaFold.	42	Emerging	413	Python
6	dptech-corp/Uni-Fold-jax Trainable AlphaFold implementation in JAX	41	Emerging	158	Python
7	wallnerlab/AFsample2 Modelling protein conformational landscape with Alphafold	37	Emerging	56	Jupyter Notebook
8	Genentech/equifold Official code repository for EquiFold: Protein Structure Prediction with a...	35	Emerging	127	Python
9	instadeepai/manyfold 🧬 ManyFold: An efficient and flexible library for training and validating...	31	Emerging	81	Python
10	colbyford/SARS-CoV-2_B.1.1.529_Spike-RBD_Predictions AlphaFold2 and RoseTTAFold predictions of the SARS-CoV-2 B.1.1.529 variant...	29	Experimental	12	Jupyter Notebook
11	dohlee/igfold-pytorch Unofficial re-implementation of IgFold, a fast antibody structure prediction...	27	Experimental	2	Python
12	FreshAirTonight/af2complex Predicting direct protein-protein interactions with AlphaFold deep learning...	25	Experimental	169	Python
13	recep2244/pdhub Protein Design Hub - ColabFold, Chai-1, Boltz-2 & OpenStructure	21	Experimental	—	Python
14	ogchen/nanofold A nano protein structure prediction model based on DeepMind's AlphaFold paper	20	Experimental	33	Python
15	Model3DBio/AF_pyDock 🧬 Integrates AlphaFold2/3 model confidence with ⚡ pyDock energy scoring to...	18	Experimental	3	Jupyter Notebook
16	LiteFold/litefold Making folding experiments more accessible .	16	Experimental	91	Python
17	shruti-sivakumar/AlphaFold-Structure-Prediction Predict 3D protein structures using AlphaFold2 via ColabFold, with...	13	Experimental	—	Jupyter Notebook