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 44 molecular structure generation models tracked. The highest-rated is MinkaiXu/GeoDiff at 49/100 with 406 stars.

Get all 44 projects as JSON

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#	Model	Score	Tier	Stars	Language
1	MinkaiXu/GeoDiff Implementation of GeoDiff: a Geometric Diffusion Model for Molecular...	49	Emerging	406	Python
2	MinkaiXu/GeoLDM Geometric Latent Diffusion Models for 3D Molecule Generation	47	Emerging	273	Python
3	caio-freitas/GraphARM An implementation of the Autoregressive Diffusion Model for Graph Generation...	46	Emerging	44	Python
4	microsoft/foldingdiff Diffusion models of protein structure; trigonometry and attention are all you need!	45	Emerging	565	Jupyter Notebook
5	Membrizard/ml_conformer_generator Shape-constrained molecule generation via Equivariant Diffusion and GCN	45	Emerging	13	Python
6	aqlaboratory/genie De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds	41	Emerging	186	Python
7	pengxingang/MolDiff MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule...	41	Emerging	89	Python
8	prescient-design/jamun Bridging Smoothed Molecular Dynamics and Score-Based Learning for...	40	Emerging	19	Python
9	HySonLab/Protein_Redesign ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant...	40	Emerging	39	Python
10	GRAPH-0/GraphGDP Implementation for the paper: GraphGDP: Generative Diffusion Processes for...	40	Emerging	32	Python
11	GRAPH-0/JODO Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation	40	Emerging	52	Python
12	eltonpan/zeosyn_gen DiffSyn: A Generative Diffusion Approach to Materials Synthesis Planning...	39	Emerging	35	Python
13	suneelbvs/DiffDock Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for...	39	Emerging	26	Jupyter Notebook
14	guanjq/targetdiff The official implementation of 3D Equivariant Diffusion for Target-Aware...	38	Emerging	324	Python
15	instadeepai/FrameDiPT FrameDiPT: an SE(3) diffusion model for protein structure inpainting	38	Emerging	58	Jupyter Notebook
16	lujiarui/Str2Str Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot...	37	Emerging	81	Python
17	20171130/Equivariant-NN-Zoo A library for building equivariant neural networks and a zoo of...	36	Emerging	32	Python
18	lamm-mit/HierarchicalDesign A computational building block approach towards multiscale architected...	35	Emerging	29	Jupyter Notebook
19	CRIPAC-DIG/tgm-dlm Code for AAAI24 paper Text-Guided Molecule Generation with Diffusion Language Model	35	Emerging	31	Python
20	YangLing0818/IPDiff [ICLR 2024] Protein-Ligand Interaction Prior for Binding-aware 3D Molecule...	35	Emerging	55	Python
21	harryjo97/GDSS Official Code Repository for the paper "Score-based Generative Modeling of...	35	Emerging	186	Python
22	YangLing0818/IRDiff [ICML 2024] Interaction-based Retrieval-augmented Diffusion Models for...	34	Emerging	34	Python
23	Lrbomchz/CoPHo Official implementation of CoPHo (KDD 2026).	33	Emerging	2	Python
24	luka-kovacevic/moracle Molecule oracle for predicting clinical viability from binding affinity and...	31	Emerging	3	Python
25	masa-ue/ProDifEvo-Refinement Evolutionary Algorithm with Diffusion Models for Protein Design	30	Emerging	30	Python
26	receptor-ai/pocket-cfdm Augmenting a training dataset of the generative diffusion model for...	30	Emerging	10	Python
27	CHNFTQ/Capricorn Capricorn: Enhancing Hi-C contact matrices for loop detection with a...	30	Emerging	8	Python
28	chao1224/GeoSSL GeoSSL: Molecular Geometry Pretraining with SE(3)-Invariant Denoising...	29	Experimental	47	Python
29	xiaoxiaokuye/CODLAD Efficient Protein Backmapping via Constraint Decoupled Latent Diffusion	28	Experimental	2	Python
30	frcnt/kldm [ICML 2025] Kinetic Langevin Diffusion for Crystalline Materials Generation	28	Experimental	3	Python
31	iakovosevdaimon/Neural-Graph-Generator Neural Graph Generator: Feature-Conditioned Graph Generation using Latent...	27	Experimental	28	Python
32	AspirinCode/DiffIUPAC Diffusion-based generative drug-like molecular editing with chemical natural language	27	Experimental	18	Python
33	TianZhuAI4S/DiffAffinity Predicting mutational effects on protein-protein binding via a side-chain...	25	Experimental	37	Jupyter Notebook
34	masa-ue/AlignInversePro Inference-Time Alignment in Protein Diffusion Models	25	Experimental	56	Jupyter Notebook
35	GRAPH-0/CDGS Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph...	23	Experimental	36	Python
36	emmamenegh/DiGress-logical-guidance Extensions of DiGress for molecular graph generation with logical...	23	Experimental	2	Python
37	frcnt/equivariant-neural-diffusion [NeurIPS 2024] Equivariant Neural Diffusion for Molecule Generation	22	Experimental	8	Python
38	Ray16/MOF_workflow Difflinker-based generative model for metal-organic frameworks (MOFs)	22	Experimental	6	Python
39	Gjphysics/thermo-moe-md-trajectory-generation Role‑constrained MoE diffusion for alanine dipeptide lagged MD dynamics and...	22	Experimental	1	Python
40	dohlee/foldingdiff-pytorch An unofficial re-implementation of FoldingDiff, a diffusion-based generative...	21	Experimental	8	Jupyter Notebook
41	YangLing0818/BindDM [AAAI 2024] Binding-Adaptive Diffusion Models for Structure-Based Drug Design	19	Experimental	20	Python
42	FarzanSoli/Protein-Structure-Generation Generating protein sequences and structures using an equivariant diffusion...	12	Experimental	—	Python
43	Shen-Lab/EBD Equivariant Blurring Diffusion for Hierarchical Molecular Conformer...	12	Experimental	7	Python
44	dohlee/diffab-pytorch An unofficial re-implementation of DiffAb, a diffusion-based generative...	11	Experimental	4	Python