Molecular Structure Generation Diffusion Models

Diffusion models for generating 3D molecular structures, materials, and chemical compounds with equivariance constraints and physics-informed priors. Does NOT include general graph generation, protein folding, or text-to-molecule without structural focus.

There are 42 molecular structure generation models tracked. The highest-rated is MinkaiXu/GeoDiff at 42/100 with 406 stars.

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#	Model	Score	Tier	Stars	Language
1	MinkaiXu/GeoDiff Implementation of GeoDiff: a Geometric Diffusion Model for Molecular...	42	Emerging	406	Python
2	MinkaiXu/GeoLDM Geometric Latent Diffusion Models for 3D Molecule Generation	40	Emerging	273	Python
3	caio-freitas/GraphARM An implementation of the Autoregressive Diffusion Model for Graph Generation...	39	Emerging	44	Python
4	Membrizard/ml_conformer_generator Shape-constrained molecule generation via Equivariant Diffusion and GCN	38	Emerging	13	Python
5	microsoft/foldingdiff Diffusion models of protein structure; trigonometry and attention are all you need!	38	Emerging	565	Jupyter Notebook
6	pengxingang/MolDiff MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule...	34	Emerging	89	Python
7	aqlaboratory/genie De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds	34	Emerging	186	Python
8	GRAPH-0/JODO Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation	33	Emerging	52	Python
9	HySonLab/Protein_Redesign ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant...	33	Emerging	39	Python
10	prescient-design/jamun Bridging Smoothed Molecular Dynamics and Score-Based Learning for...	33	Emerging	19	Python
11	GRAPH-0/GraphGDP Implementation for the paper: GraphGDP: Generative Diffusion Processes for...	33	Emerging	32	Python
12	suneelbvs/DiffDock Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for...	32	Emerging	26	Jupyter Notebook
13	eltonpan/zeosyn_gen DiffSyn: A Generative Diffusion Approach to Materials Synthesis Planning...	32	Emerging	35	Python
14	guanjq/targetdiff The official implementation of 3D Equivariant Diffusion for Target-Aware...	31	Emerging	324	Python
15	instadeepai/FrameDiPT FrameDiPT: an SE(3) diffusion model for protein structure inpainting	31	Emerging	58	Jupyter Notebook
16	lujiarui/Str2Str Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot...	30	Emerging	81	Python
17	Lrbomchz/CoPHo Official implementation of CoPHo (KDD 2026).	29	Experimental	2	Python
18	20171130/Equivariant-NN-Zoo A library for building equivariant neural networks and a zoo of...	29	Experimental	32	Python
19	CRIPAC-DIG/tgm-dlm Code for AAAI24 paper Text-Guided Molecule Generation with Diffusion Language Model	28	Experimental	31	Python
20	harryjo97/GDSS Official Code Repository for the paper "Score-based Generative Modeling of...	28	Experimental	186	Python
21	YangLing0818/IPDiff [ICLR 2024] Protein-Ligand Interaction Prior for Binding-aware 3D Molecule...	28	Experimental	55	Python
22	lamm-mit/HierarchicalDesign A computational building block approach towards multiscale architected...	28	Experimental	29	Jupyter Notebook
23	masa-ue/ProDifEvo-Refinement Evolutionary Algorithm with Diffusion Models for Protein Design	27	Experimental	30	Python
24	YangLing0818/IRDiff [ICML 2024] Interaction-based Retrieval-augmented Diffusion Models for...	27	Experimental	34	Python
25	luka-kovacevic/moracle Molecule oracle for predicting clinical viability from binding affinity and...	24	Experimental	3	Python
26	CHNFTQ/Capricorn Capricorn: Enhancing Hi-C contact matrices for loop detection with a...	23	Experimental	8	Python
27	receptor-ai/pocket-cfdm Augmenting a training dataset of the generative diffusion model for...	23	Experimental	10	Python
28	frcnt/kldm [ICML 2025] Kinetic Langevin Diffusion for Crystalline Materials Generation	22	Experimental	3	Python
29	chao1224/GeoSSL GeoSSL: Molecular Geometry Pretraining with SE(3)-Invariant Denoising...	22	Experimental	47	Python
30	masa-ue/AlignInversePro Inference-Time Alignment in Protein Diffusion Models	22	Experimental	56	Jupyter Notebook
31	xiaoxiaokuye/CODLAD Efficient Protein Backmapping via Constraint Decoupled Latent Diffusion	21	Experimental	2	Python
32	Gjphysics/thermo-moe-md-trajectory-generation Role‑constrained MoE diffusion for alanine dipeptide lagged MD dynamics and...	20	Experimental	1	Python
33	iakovosevdaimon/Neural-Graph-Generator Neural Graph Generator: Feature-Conditioned Graph Generation using Latent...	20	Experimental	28	Python
34	AspirinCode/DiffIUPAC Diffusion-based generative drug-like molecular editing with chemical natural language	20	Experimental	18	Python
35	TianZhuAI4S/DiffAffinity Predicting mutational effects on protein-protein binding via a side-chain...	18	Experimental	37	Jupyter Notebook
36	dohlee/foldingdiff-pytorch An unofficial re-implementation of FoldingDiff, a diffusion-based generative...	17	Experimental	8	Jupyter Notebook
37	emmamenegh/DiGress-logical-guidance Extensions of DiGress for molecular graph generation with logical...	17	Experimental	2	Python
38	GRAPH-0/CDGS Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph...	16	Experimental	36	Python
39	frcnt/equivariant-neural-diffusion [NeurIPS 2024] Equivariant Neural Diffusion for Molecule Generation	15	Experimental	8	Python
40	Ray16/MOF_workflow Difflinker-based generative model for metal-organic frameworks (MOFs)	15	Experimental	6	Python
41	YangLing0818/BindDM [AAAI 2024] Binding-Adaptive Diffusion Models for Structure-Based Drug Design	12	Experimental	20	Python
42	FarzanSoli/Protein-Structure-Generation Generating protein sequences and structures using an equivariant diffusion...	12	Experimental	—	Python