Protein Engineering Design ML Frameworks

Tools for computationally designing and optimizing proteins through mutation, folding prediction, and binding affinity engineering—including antibodies, enzymes, and synthetic binders. Does NOT include general protein structure prediction, sequence alignment, or property prediction without design objectives.

There are 28 protein engineering design frameworks tracked. 3 score above 50 (established tier). The highest-rated is Graylab/DL4Proteins-notebooks at 64/100 with 659 stars. 2 of the top 10 are actively maintained.

Get all 28 projects as JSON

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

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#	Framework	Score	Tier	Stars	Language
1	Graylab/DL4Proteins-notebooks Colab Notebooks covering deep learning tools for biomolecular structure...	64	Established	659	Jupyter Notebook
2	Peldom/papers_for_protein_design_using_DL List of papers about Proteins Design using Deep Learning	56	Established	1,898	—
3	rdk/p2rank P2Rank: Protein-ligand binding site prediction from protein structure based...	51	Established	399	Groovy
4	llnl/protlib-designer Integer Linear Programming for Protein Library Design	49	Emerging	9	Python
5	samsinai/FLEXS Fitness landscape exploration sandbox for biological sequence design.	47	Emerging	170	Jupyter Notebook
6	LBM-EPFL/CARBonAra Deep learning framework for protein sequence design from a backbone scaffold...	40	Emerging	48	Jupyter Notebook
7	20n/act Computational synthetic biology: Predicting DNA edits for bioengineering	38	Emerging	91	Java
8	Mohamed5352/proteindj 🧬 Design proteins efficiently with ProteinDJ, a Nextflow pipeline...	37	Emerging	3	Python
9	Genentech/walk-jump Official repository for discrete Walk-Jump Sampling (dWJS)	34	Emerging	56	Python
10	haddocking/DeepRank-Ab Repository of the DeepRank-Ab AI model and software for scoring...	34	Emerging	17	Python
11	kevinmicha/ANTIPASTI ANTIPASTI (ANTIbody Predictor of Affinity from STructural Information) is a...	33	Emerging	39	Jupyter Notebook
12	prescient-design/holo-bench Benchmark for Biophysical Sequence Optimization Algorithms	32	Emerging	20	Python
13	prescient-design/walk-jump Official repository for discrete Walk-Jump Sampling (dWJS)	32	Emerging	59	JavaScript
14	AtharvaTilewale/boltz2-notebook Boltz2 Notebook – A streamlined Colab-based pipeline for protein structure...	32	Emerging	8	HTML
15	jianqingzheng/XBCR-net [Cell Research] Deep learning-based rapid generation of broadly reactive...	28	Experimental	32	Python
16	vector-engineering/fit4function Systematic Multi-Trait AAV Capsid Engineering for Efficient Gene Delivery...	28	Experimental	11	Jupyter Notebook
17	Hollfelder-Lab/lrDMS-IRED Code, data and notebooks for engineering enzymes with ultra-high throughput...	27	Experimental	10	Jupyter Notebook
18	denisbeslic/denovopipeline Pipeline for de novo peptide sequencing (Novor, DeepNovo, SMSNet, PointNovo,...	26	Experimental	44	Python
19	duerrsimon/mars-biohackathon Predicting thermostability using a VAE and prediction from the latent space.	26	Experimental	6	HTML
20	FedericoPivotto/viraminer-cb ViraMiner-CB: Deep Learning Architecture Inspired from GoogleLeNet for...	24	Experimental	4	Jupyter Notebook
21	CANOLIO/antarctic-fungi-ml Computational bioprospecting pipeline for the identification of cold-active...	22	Experimental	—	Python
22	mit-ll/AlphaSeq_Antibody_Dataset Dataset with quantitative binding scores of scFv-format antibodies against...	18	Experimental	26	—
23	bayer-science-for-a-better-life/topefind-public Finding the pitfalls of deep learning predictors of interacting residues in...	17	Experimental	24	Python
24	TheDogDanydel/protmind 🧬 Enhance protein structure analysis with ProtMind’s AI-driven tools for...	16	Experimental	—	—
25	olakalisz/adios Code for ADIOS: Antibody Development via Opponent Shaping	15	Experimental	7	Python
26	ImaginaryLogs/CSC713M-CROWN19AB-PROJECT A machine learning model studying antibody neutralization and binding to...	14	Experimental	—	Jupyter Notebook
27	martin-he543/novozymes-enzyme-stability-prediction-kaggle-2022 The Kaggle team for the Novozymes Enzyme Stability Prediction Machine...	13	Experimental	8	Jupyter Notebook
28	Kaz-bits/Machine-learning-protein-design This repository contains the scripts to create a ML algorithm for protein...	10	Experimental	1	Shell