Drug Discovery ML ML Frameworks

Tools and frameworks for AI-driven drug discovery, repurposing, and virtual screening—including molecular interaction prediction, binding affinity modeling, and compound prioritization. Does NOT include general drug response prediction in existing cell lines, cancer pharmacogenomics, or therapeutic outcome modeling.

There are 55 drug discovery ml frameworks tracked. 1 score above 70 (verified tier). The highest-rated is ersilia-os/ersilia at 72/100 with 291 stars and 464 monthly downloads. 1 of the top 10 are actively maintained.

Get all 55 projects as JSON

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

Open to everyone — 100 requests/day, no key needed. Get a free key for 1,000/day.

#	Framework	Score	Tier	Stars	Language
1	ersilia-os/ersilia The Ersilia Model Hub, a repository of AI/ML models for infectious and...	72	Verified	291	Python
2	NVIDIA/bionemo-framework BioNeMo Framework: For building and adapting AI models in drug discovery at scale	58	Established	679	Jupyter Notebook
3	PNNL-CompBio/coderdata Dataset package for facile training and testing of machine learning/AI...	54	Established	20	Jupyter Notebook
4	adosar/aidsorb Python package for deep learning on molecular point clouds.	51	Established	6	Python
5	RyanWangZf/PyTrial PyTrial: A Comprehensive Platform for Artificial Intelligence for Drug Development	48	Emerging	124	Python
6	nrflynn2/ml-drug-discovery The official repository for the book "Machine Learning for Drug Discovery"...	47	Emerging	70	Jupyter Notebook
7	CDDLeiden/DrugEx De Novo Drug Design with RNNs and Transformers	47	Emerging	173	Jupyter Notebook
8	mims-harvard/TDC Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science	45	Emerging	1,215	Jupyter Notebook
9	nf-core/drugresponseeval Pipeline for testing drug response prediction models in a statistically and...	42	Emerging	24	Nextflow
10	DeepGraphLearning/torchdrug A powerful and flexible machine learning platform for drug discovery	41	Emerging	1,570	Python
11	topazape/LSTM_Chem Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.	41	Emerging	118	Jupyter Notebook
12	daisybio/drevalpy DrEval is a toolkit that ensures drug response prediction evaluations are...	40	Emerging	32	Python
13	benedekrozemberczki/tigerlily TigerLily: Finding drug interactions in silico with the Graph.	39	Emerging	100	Jupyter Notebook
14	asapdiscovery/asapdiscovery Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium	37	Emerging	46	Python
15	Institute-for-Future-Intelligence/aims AIMS: Artificial Intelligence for Molecular Sciences	35	Emerging	4	TypeScript
16	canela0208/ai-drug-discovery-slides 🧬 Explore AI-driven drug discovery through an interactive presentation...	35	Emerging	1	Jupyter Notebook
17	JieZheng-ShanghaiTech/KG4SL Synthetic lethality (SL) is a promising gold mine for the discovery of...	34	Emerging	33	Python
18	nghiencuuthuoc/PharmApp PharmApp - 🧠 AI for Research and Development Pharmaceuticals	34	Emerging	2	Jupyter Notebook
19	francescopatane96/Computer_aided_drug_discovery_kit This pipeline provides a way to perform pharmaceutical compounds virtual...	33	Emerging	23	Jupyter Notebook
20	SeonghwanSeo/PharmacoNet Official Github for "PharmacoNet: deep learning-guided pharmacophore...	33	Emerging	88	Python
21	AstraZeneca/awesome-drug-pair-scoring Readings for "A Unified View of Relational Deep Learning for Drug Pair...	33	Emerging	98	—
22	burakcan-izmirli/DeepResponse DeepResponse: Large Scale Prediction of Cancer Cell Line Drug Response with...	32	Emerging	6	Python
23	molML/s4-for-de-novo-drug-design The official codebase of the paper "Chemical language modeling with...	30	Emerging	88	HTML
24	rezacsedu/Drug-Drug-Interaction-Prediction Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and...	30	Emerging	99	Jupyter Notebook
25	farhad-abdi/InSilicoQ Quantum Computing and Machine Learning for Drug Design and Proteins Engineering	29	Experimental	14	Python
26	dlopezyse/Drug-Repurposing-using-KGE 💊 Drug repurposing using knowledge graph embeddings with a focus on...	28	Experimental	8	HTML
27	mathcom/MolBit De novo Drug Design via Binary Representations of SMILES for avoiding the...	27	Experimental	8	Jupyter Notebook
28	aidd-msca/aidd-codebase Public version of the AIDD consortium code base	26	Experimental	11	—
29	kamilpytlak/InhibiPro 🧪 InhibiPro - a web-based application for predicting the pharmacological...	24	Experimental	2	PureBasic
30	JinYSun/D-GCAN Methods of druglikeness prediction	24	Experimental	16	Jupyter Notebook
31	SeonghwanSeo/OpenPharmaco Open-source protein-based pharmacophore modeling software	24	Experimental	37	Python
32	ersilia-os/ersilia-intro-workshop This is an introductory course to AI/ML applied to drug discovery	23	Experimental	2	Jupyter Notebook
33	PeijingZhang/Shennong A deep-learning framework to predict the tumor-associated cells' reaction to...	23	Experimental	8	Jupyter Notebook
34	steffanhoez/Arr-Medic-CYP3A4 🧬 Predict drug interactions with the open-source CYP3A4 system, essential...	23	Experimental	1	Python
35	MATZGLCH/BioSyn-AI-Repurposing-Life 🌱 Unlock new cancer and rare disease treatments through AI-driven drug...	22	Experimental	—	—
36	Jameshuff91/open-cure Complementary open-source drug repurposing research using AI and biomedical...	22	Experimental	—	Python
37	Srilaxman05/open-cure-discovery 🔍 Accelerate drug discovery with open-source, GPU-driven virtual screening...	22	Experimental	—	Python
38	smb-h/de-novo-drug-discovery De Novo Drug Design	21	Experimental	2	Jupyter Notebook
39	JieZheng-ShanghaiTech/PiLSL PiLSL is a pairwise interaction learning-based graph neural network (GNN)...	20	Experimental	12	Python
40	molML/chemical-language-processing-for-bioactivity-prediction The official codebase for the paper "A Hitchhiker's Guide to Deep Chemical...	20	Experimental	11	Python
41	NilavoBoral/Therapeutics-Data-Commons Single-instance Prediction of small-molecule drug.	19	Experimental	6	Jupyter Notebook
42	mcamposcarneros/Molecular-Predictive-Discovery AI-driven virtual screening platform for molecular interaction prediction...	19	Experimental	—	Jupyter Notebook
43	flexycode/BIOF-101 💫 BIOINFORMATICS for Drug Development	18	Experimental	3	—
44	RohanV01/Drug-Discovery-Toolkit-for-beginners This repository talks about basic concepts of Bioinformatics and...	17	Experimental	5	—
45	famenaghawon/drug-response-prediction 💊 Advanced Drug Response Prediction & Multi-Omics Platform Interactive...	16	Experimental	1	Jupyter Notebook
46	anastev982/anti-cancer-drug-effectiveness From raw biomedical data to predictive modeling: a machine learning pipeline...	14	Experimental	—	Python
47	JyotismoyKalita/DrugDetectClassify-IITG A Drug Detection model and a Drug Classification model using Logistic...	14	Experimental	3	Jupyter Notebook
48	billy-enrizky/response-to-steroid Predicting Response to Steroid using Multimodal Deep Learning Model	13	Experimental	2	Jupyter Notebook
49	zbarry/pytorch-hcs Predict drug mechanism of action from high content screening images using PyTorch	13	Experimental	7	Jupyter Notebook
50	PeeteKeesel/gnn-for-drug-response-prediction :dna: Process repository for my master thesis attacking drug response...	13	Experimental	8	Jupyter Notebook
51	aion-labs/aiondata A common data access layer for AI-driven drug discovery.	12	Experimental	—	Python
52	ShengyaoLiang/StellarCodeBio Pioneering Next-Generation AI for Scientific Breakthroughs. Starting with a...	12	Experimental	1	Python
53	techthumb1/KGNN-Drug-Drug-Interaction-DDI-Prediction A deep learning application for predicting drug-drug interactions using...	11	Experimental	—	Jupyter Notebook
54	DogInfantry/Dstonks Global Life Sciences & Health Technologies Outlook (2026-2035) Strategic...	11	Experimental	—	Jupyter Notebook
55	nghiencuuthuoc/PharmAI PharmAI are tools for Artificial intelligence in drug discovery and development	10	Experimental	1	—