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

Get all 53 projects as JSON

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#	Framework	Score	Tier	Stars	Language
1	ersilia-os/ersilia The Ersilia Model Hub, a repository of AI/ML models for infectious and...	70	Verified	291	Python
2	NVIDIA/bionemo-framework BioNeMo Framework: For building and adapting AI models in drug discovery at scale	62	Established	679	Jupyter Notebook
3	PNNL-CompBio/coderdata Dataset package for facile training and testing of machine learning/AI...	56	Established	20	Jupyter Notebook
4	RyanWangZf/PyTrial PyTrial: A Comprehensive Platform for Artificial Intelligence for Drug Development	55	Established	124	Python
5	CDDLeiden/DrugEx De Novo Drug Design with RNNs and Transformers	54	Established	173	Jupyter Notebook
6	adosar/aidsorb Python package for deep learning on molecular point clouds.	52	Established	6	Python
7	mims-harvard/TDC Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science	52	Established	1,215	Jupyter Notebook
8	nrflynn2/ml-drug-discovery The official repository for the book "Machine Learning for Drug Discovery"...	50	Established	70	Jupyter Notebook
9	nf-core/drugresponseeval Pipeline for testing drug response prediction models in a statistically and...	49	Emerging	24	Nextflow
10	DeepGraphLearning/torchdrug A powerful and flexible machine learning platform for drug discovery	48	Emerging	1,570	Python
11	topazape/LSTM_Chem Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.	48	Emerging	118	Jupyter Notebook
12	benedekrozemberczki/tigerlily TigerLily: Finding drug interactions in silico with the Graph.	46	Emerging	100	Jupyter Notebook
13	daisybio/drevalpy DrEval is a toolkit that ensures drug response prediction evaluations are...	44	Emerging	32	Python
14	JieZheng-ShanghaiTech/KG4SL Synthetic lethality (SL) is a promising gold mine for the discovery of...	41	Emerging	33	Python
15	nghiencuuthuoc/PharmApp PharmApp - 🧠 AI for Research and Development Pharmaceuticals	41	Emerging	2	Jupyter Notebook
16	canela0208/ai-drug-discovery-slides 🧬 Explore AI-driven drug discovery through an interactive presentation...	41	Emerging	1	Jupyter Notebook
17	asapdiscovery/asapdiscovery Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium	41	Emerging	46	Python
18	AstraZeneca/awesome-drug-pair-scoring Readings for "A Unified View of Relational Deep Learning for Drug Pair...	40	Emerging	98	—
19	francescopatane96/Computer_aided_drug_discovery_kit This pipeline provides a way to perform pharmaceutical compounds virtual...	40	Emerging	23	Jupyter Notebook
20	SeonghwanSeo/PharmacoNet Official Github for "PharmacoNet: deep learning-guided pharmacophore...	40	Emerging	88	Python
21	burakcan-izmirli/DeepResponse DeepResponse: Large Scale Prediction of Cancer Cell Line Drug Response with...	39	Emerging	6	Python
22	molML/s4-for-de-novo-drug-design The official codebase of the paper "Chemical language modeling with...	37	Emerging	88	HTML
23	rezacsedu/Drug-Drug-Interaction-Prediction Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and...	37	Emerging	99	Jupyter Notebook
24	farhad-abdi/InSilicoQ Quantum Computing and Machine Learning for Drug Design and Proteins Engineering	36	Emerging	14	Python
25	mathcom/MolBit De novo Drug Design via Binary Representations of SMILES for avoiding the...	34	Emerging	8	Jupyter Notebook
26	aidd-msca/aidd-codebase Public version of the AIDD consortium code base	33	Emerging	11	—
27	JinYSun/D-GCAN Methods of druglikeness prediction	31	Emerging	16	Jupyter Notebook
28	SeonghwanSeo/OpenPharmaco Open-source protein-based pharmacophore modeling software	31	Emerging	37	Python
29	kamilpytlak/InhibiPro 🧪 InhibiPro - a web-based application for predicting the pharmacological...	31	Emerging	2	PureBasic
30	ersilia-os/ersilia-intro-workshop This is an introductory course to AI/ML applied to drug discovery	30	Emerging	2	Jupyter Notebook
31	PeijingZhang/Shennong A deep-learning framework to predict the tumor-associated cells' reaction to...	30	Emerging	8	Jupyter Notebook
32	steffanhoez/Arr-Medic-CYP3A4 🧬 Predict drug interactions with the open-source CYP3A4 system, essential...	30	Emerging	1	Python
33	aion-labs/aiondata A common data access layer for AI-driven drug discovery.	28	Experimental	—	Python
34	smb-h/de-novo-drug-discovery De Novo Drug Design	28	Experimental	2	Jupyter Notebook
35	molML/chemical-language-processing-for-bioactivity-prediction The official codebase for the paper "A Hitchhiker's Guide to Deep Chemical...	27	Experimental	11	Python
36	JieZheng-ShanghaiTech/PiLSL PiLSL is a pairwise interaction learning-based graph neural network (GNN)...	27	Experimental	12	Python
37	NilavoBoral/Therapeutics-Data-Commons Single-instance Prediction of small-molecule drug.	26	Experimental	6	Jupyter Notebook
38	flexycode/BIOF-101 💫 BIOINFORMATICS for Drug Development	25	Experimental	3	—
39	RohanV01/Drug-Discovery-Toolkit-for-beginners This repository talks about basic concepts of Bioinformatics and...	24	Experimental	5	—
40	Srilaxman05/open-cure-discovery 🔍 Accelerate drug discovery with open-source, GPU-driven virtual screening...	22	Experimental	—	Python
41	Jameshuff91/open-cure Complementary open-source drug repurposing research using AI and biomedical...	22	Experimental	—	Python
42	mcamposcarneros/Molecular-Predictive-Discovery AI-driven virtual screening platform for molecular interaction prediction...	21	Experimental	—	Jupyter Notebook
43	zbarry/pytorch-hcs Predict drug mechanism of action from high content screening images using PyTorch	20	Experimental	7	Jupyter Notebook
44	JyotismoyKalita/DrugDetectClassify-IITG A Drug Detection model and a Drug Classification model using Logistic...	20	Experimental	3	Jupyter Notebook
45	PeeteKeesel/gnn-for-drug-response-prediction :dna: Process repository for my master thesis attacking drug response...	20	Experimental	8	Jupyter Notebook
46	billy-enrizky/response-to-steroid Predicting Response to Steroid using Multimodal Deep Learning Model	19	Experimental	2	Jupyter Notebook
47	ShengyaoLiang/StellarCodeBio Pioneering Next-Generation AI for Scientific Breakthroughs. Starting with a...	18	Experimental	1	Python
48	MengjieChan/MolecBioNet Towards Interpretable Drug-Drug Interaction Prediction: A Graph-Based...	14	Experimental	6	Python
49	anastev982/anti-cancer-drug-effectiveness From raw biomedical data to predictive modeling: a machine learning pipeline...	14	Experimental	—	Python
50	DogInfantry/Dstonks Global Life Sciences & Health Technologies Outlook (2026-2035) Strategic...	13	Experimental	—	Jupyter Notebook
51	techthumb1/KGNN-Drug-Drug-Interaction-DDI-Prediction A deep learning application for predicting drug-drug interactions using...	13	Experimental	—	Jupyter Notebook
52	HawkPhantom/mechanisms_of_action_prediction Deep Learning Algorithm to classify drugs based on their biological activity.	11	Experimental	—	R
53	IvanBuccella/SF2Bio Deep reinforcement learning for de novo drug design: a ReLeaSe method...	11	Experimental	—	Dockerfile

Comparisons in this category

DrugEx and LSTM_Chem (54 vs 48)