3D Molecule Generation

Benchmarks archive 2025-07-28

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Datasets archive 2025-07-28

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Most implemented papers archive 2025-07-28

22 shown of 22 papers with code (37 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• Geometry-Complete Diffusion for 3D Molecule Generation and Optimization
  8 Feb 2023 3 repositories listed Syntology ran 3 of 10 samples · 7 unverified
  Importantly, we demonstrate that the geometry-complete denoising process of GCDM learned for 3D molecule generation enables the model to generate a significant proportion of valid and energetically-stable large…
• Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation
  30 Apr 2024 2 repositories listed
  In this work, we explore the use of flow matching, a recently proposed generative modeling framework that generalizes diffusion models, for the task of de novo molecule generation.
• Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation
  21 May 2023 2 repositories listed Syntology ran 3 of 4 samples · 1 unverified · 3 pointer-only (licence)
  To capture the correlation between molecular graphs and geometries in the diffusion process, we develop a Diffusion Graph Transformer to parameterize the data prediction model that recovers the original data from noisy…
• Geometric Latent Diffusion Models for 3D Molecule Generation
  2 May 2023 2 repositories listed Syntology ran 4 of 9 samples · 5 unverified
  Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design.
• Graph Generation with Diffusion Mixture
  7 Feb 2023 2 repositories listed Syntology ran 2 of 4 samples · 2 unverified · 4 pointer-only (licence)
  Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures.
• Equivariant Energy-Guided SDE for Inverse Molecular Design
  30 Sep 2022 2 repositories listed Syntology ran 0 of 2 samples · 2 unverified · 2 pointer-only (licence)
  Inverse molecular design is critical in material science and drug discovery, where the generated molecules should satisfy certain desirable properties.
• Scalable Non-Equivariant 3D Molecule Generation via Rotational Alignment
  11 Jun 2025 1 repository listed
  Equivariant diffusion models have achieved impressive performance in 3D molecule generation.
• GEOM-Drugs Revisited: Toward More Chemically Accurate Benchmarks for 3D Molecule Generation
  30 Apr 2025 1 repository listed
  Deep generative models have shown significant promise in generating valid 3D molecular structures, with the GEOM-Drugs dataset serving as a key benchmark.
• Straight-Line Diffusion Model for Efficient 3D Molecular Generation
  4 Mar 2025 1 repository listed Syntology ran 2 of 4 samples · 2 unverified
  Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples.
• ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation
  20 Feb 2025 1 repository listed
  Protein backbone generation plays a central role in de novo protein design and is significant for many biological and medical applications.
• NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation
  18 Feb 2025 1 repository listed
  To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation.
• BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation
  26 Jan 2025 1 repository listed
  To address alignment challenges, we introduce a method that relocates the center of mass of generated ligands to their docking poses, enabling accurate sub-component extraction.
• Score-based 3D molecule generation with neural fields
  15 Jan 2025 1 repository listed Syntology ran 5 of 8 samples · 3 unverified · 8 pointer-only (licence)
  Using this representation, we propose a new model based on walk-jump sampling for unconditional 3D molecule generation in the continuous space using neural fields.
• D3MES: Diffusion Transformer with multihead equivariant self-attention for 3D molecule generation
  13 Jan 2025 1 repository listed
  Understanding and predicting the diverse conformational states of molecules is crucial for advancing fields such as chemistry, material science, and drug development.
• BInD: Bond and Interaction-generating Diffusion Model for Multi-objective Structure-based Drug Design
  27 May 2024 1 repository listed
  A remarkable advance in geometric deep generative models with accumulated structural data enables structure-based drug design (SBDD) with target protein information only.
• Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks
  17 Mar 2024 1 repository listed
  Advanced generative model (e.
• Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation
  5 Jan 2024 1 repository listed Syntology ran 13 of 13 samples · 0 unverified
  The second challenge involves accommodating molecule generation to diffusion and accurately predicting the existence of bonds.
• Symphony: Symmetry-Equivariant Point-Centered Spherical Harmonics for 3D Molecule Generation
  27 Nov 2023 1 repository listed Syntology ran 1 of 1 samples · 0 unverified
  We present Symphony, an E(3)-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments.
• 3D molecule generation by denoising voxel grids
  13 Jun 2023 1 repository listed Syntology ran 0 of 7 samples · 7 unverified
  We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids.
• Learning Subpocket Prototypes for Generalizable Structure-based Drug Design
  22 May 2023 1 repository listed Syntology ran 1 of 2 samples · 1 unverified · 2 pointer-only (licence)
  Generating molecules with high binding affinities to target proteins (a.
• MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation
  11 May 2023 1 repository listed Syntology ran 5 of 15 samples · 10 unverified
  Deep generative models have recently achieved superior performance in 3D molecule generation.
• GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow
  23 Feb 2023 1 repository listed
  In particular, GraphVF represents the first controllable geometry-aware, protein-specific molecule generation method, which can generate binding 3D molecules with tailored sub-structures and physio-chemical properties.

Syntology lines on 12 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced. Read from the graph 2026-09-24.