Molecular Structure Design Generative AI Tools

Tools for AI-driven design of molecules, antibodies, and proteins with 3D structure prediction, binding affinity optimization, and drug discovery applications. Does NOT include general molecular simulation, protein folding prediction, or docking/binding site analysis without generative components.

There are 48 molecular structure design tools tracked. 5 score above 50 (established tier). The highest-rated is microsoft/mattergen at 67/100 with 1,643 stars and 184 monthly downloads. 2 of the top 10 are actively maintained.

Get all 48 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=generative-ai&subcategory=molecular-structure-design&limit=20"

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#	Tool	Score	Tier	Stars	Language
1	microsoft/mattergen Official implementation of MatterGen -- a generative model for inorganic...	67	Established	1,643	Python
2	MorganCThomas/MolScore An automated scoring function to facilitate and standardize the evaluation...	63	Established	225	Python
3	MolecularAI/REINVENT4 AI molecular design tool for de novo design, scaffold hopping, R-group...	61	Established	707	Python
4	AspirinCode/papers-for-molecular-design-using-DL List of Molecular and Material design using Generative AI and Deep Learning	59	Established	925	—
5	pregHosh/MolCraftDiffusion A generative AI framework for 3D molecular generation and data-driven...	52	Established	13	Python
6	Liu-Group-UF/PropMolFlow SE(3) Equivariant Flow Matching for Property-Guided Conditional Molecular Generation.	42	Emerging	53	Python
7	coleygroup/shepherd Training and inference code for ShEPhERD: Diffusing shape, electrostatics,...	41	Emerging	91	Python
8	FERMat-ML/OMatG State-of-the-art generative model for crystal structure prediction and de...	41	Emerging	45	Python
9	mims-harvard/ProCyon ProCyon: A multimodal foundation model for protein phenotypes	41	Emerging	56	Python
10	EDAPINENUT/CBGBench Official code repository of < CBGBench: Fill in the Blank of...	38	Emerging	324	Python
11	THUNLP-MT/dyMEAN This repo contains the codes for our paper "End-to-End Full-Atom Antibody Design"	36	Emerging	126	Python
12	THUNLP-MT/MEAN This repo contains the codes for our paper Conditional Antibody Design as 3D...	36	Emerging	103	Python
13	JanoschMenke/metis Python-based GUI to collect Feedback of Chemist in Molecules	35	Emerging	53	Python
14	lujiarui/esmdiff Codebase of paper "Structure Language Models for Protein Conformation...	35	Emerging	74	Python
15	jssweller/DrugHIVE DrugHIVE: Structure-based drug design with a deep hierarchical generative model	33	Emerging	111	Python
16	THUNLP-MT/PepGLAD Codes for our paper "Full-Atom Peptide Design with Geometric Latent...	31	Emerging	109	Python
17	AngxiaoYue/ReQFlow [ICML 2025] 🧬 ReQFlow: Rectified Quaternion Flow for Efficient and...	30	Emerging	81	Python
18	NilsDunlop/PROTACFold A toolkit developed to predict and analyze PROTAC-mediated ternary complexes...	29	Experimental	41	Python
19	brsynth/molecule-signature Signature based molecule enumeration from morgan fingerprints	28	Experimental	1	Python
20	LirongWu/RAAD Code for AAAI 2025 paper "Relation-Aware Equivariant Graph Networks for...	28	Experimental	5	C++
21	EDAPINENUT/ppflow This repository is the official code source of PPFlow: Target-Aware Peptide...	27	Experimental	91	Python
22	EDAPINENUT/GeoAB This is the official repository of paper - GeoAB: Towards Realistic...	26	Experimental	43	Python
23	pfizer-opensource/e3moldiffusion Research repository for diffusion based structure based drug design	26	Experimental	27	Jupyter Notebook
24	technion-cs-nlp/BetaReconstruct Ancestral sequence reconstruction using generative models	25	Experimental	2	Python
25	mnjirjak/ml_peptide_self_assembly AI models for prediction and design of novel self-assembling peptides	25	Experimental	5	Python
26	ThomasGust/Molecumixer Very incomplete right now, pretrained ARGVAET system for generating,...	25	Experimental	5	Python
27	HySonLab/DrugPipe DrugPipe: Generative artificial intelligence-assisted virtual screening...	24	Experimental	17	Python
28	mieskolainen/AIMS25 Synthetic Quantum Electrodynamics via Generative AI @ AIMS, Cape Town, May 2025	24	Experimental	7	Jupyter Notebook
29	Paulhb7/orphafold 🧬 OrphaFold is an AI-powered platform designed to accelerate research into...	24	Experimental	1	TypeScript
30	zaixizhang/FLAG Implementation of ICLR23 paper "Molecule Generation for Target Protein...	23	Experimental	72	Python
31	ewijaya/gflownet-peptide GFlowNet-based therapeutic peptide design. Generates diverse, high-quality...	22	Experimental	3	Python
32	kari15/GENOVA-pytorch GENOVA is an AI-driven de novo drug design framework based on WGAN-GP and...	22	Experimental	—	Python
33	HySonLab/Ligand_Generation Target-aware Variational Auto-encoders for Ligand Generation with Multimodal...	21	Experimental	32	Python
34	gersteinlab/GenAI4Drug [Briefings in Bioinformatics] A Survey of Generative AI for de novo Drug Design	20	Experimental	96	—
35	SamuelYueYu/QO-BRA_1.0 Quantum Operator-Based Real-Amplitude autoencoder (QOBRA) for generating...	20	Experimental	1	Jupyter Notebook
36	HySonLab/MGVAE Higher-order permutation-equivariant graph variational autoencoder to...	18	Experimental	3	Python
37	izgys/miniprotein-binder-rfdiffusion De novo design of a miniprotein binder targeting the SARS-CoV-2 spike RBD...	17	Experimental	2	Python
38	ovitrac/radigen Radigen 🧪⚛️: Python-based chemical kernel for simulating oxidation reactions...	16	Experimental	1	HTML
39	HySonLab/EvoSynth EvoSynth: Enabling Multi-Target Drug Discovery through Latent Evolutionary...	15	Experimental	7	Jupyter Notebook
40	PoraminSukyaruek/BioSynther 🧬 Create optimized biological systems with BioSynther, an AI-driven platform...	14	Experimental	—	Python
41	ayushnoori/molecule-synthesis Multi-objective generative AI for designing novel brain-targeting small molecules.	13	Experimental	8	Jupyter Notebook
42	slimgroup/WISE.jl WISE: full-Waveform variational Inference via Subsurface Extensions	12	Experimental	3	Julia
43	TarqIQ/ChemInstruct Chemical Named Entity Recognition Training and Testing Tool	12	Experimental	—	Python
44	Adam-maz/CB2-CADD-toolkit A toolkit for molecular generation, QSAR prediction (GNN-based), and...	11	Experimental	—	Jupyter Notebook
45	machinestein/General-Cost-Neural-Optimal-Transport Official Pytorch implementation of "Neural Optimal Transport with General...	11	Experimental	24	Jupyter Notebook
46	zwang1995/solvent-VAE-NLP Molecular design of solvents coupling variational autoencoder and nonlinear...	11	Experimental	2	Python
47	gortegam/FMO-GenAI-QuantumDynamics Generative AI–assisted simulation of quantum coherence and energy transfer...	11	Experimental	—	Python
48	chenebuah/EVAPD A deep evolutionary learning framework for discovering stable and...	10	Experimental	1	Python

Comparisons in this category

MEAN and dyMEAN (36 vs 36)