Awesome q-bio.BM

Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design (2026)

Xiaoliang Shi et al.

4.33

Enerzyme: A Framework for Efficient Training of Reactive Neural Network Potentials for Enzyme Catalysis with Application to Methyltransferases (2026)

Weiliang Luo et al.

3.45

MolSight: A Graph-Aware Vision-Language Model for Unified Chemical Image Understanding (2026)

Wenda Wang et al.

1.94

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design (2026)

Chen Wei et al.

1.83

Bridging the Simulation-to-Experiment Gap with Generative Models using Adversarial Distribution Alignment (2026)

Kai Nelson et al.

1.78

Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation (2026)

Cai Zhou et al.

1.67

CryoNet.Refine: A One-step Diffusion Model for Rapid Refinement of Structural Models with Cryo-EM Density Map Restraints (2026)

Fuyao Huang et al.

1.67

Unlocking hidden biomolecular conformational landscapes in diffusion models at inference time (2025)

Daniel D. Richman et al.

1.56

Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules versus Therapeutic Peptides (2025)

Yiquan Wang et al.

1.50

Torsion-Space Diffusion for Protein Backbone Generation with Geometric Refinement (2025)

Lakshaditya Singh et al.

1.50

Flow Autoencoders are Effective Protein Tokenizers (2025)

Rohit Dilip et al.

1.44

Constrained Diffusion for Protein Design with Hard Structural Constraints (2025)

Jacob K. Christopher et al.

1.44

Flows, straight but not so fast: Exploring the design space of Rectified Flows in Protein Design (2025)

Junhua Chen et al.

1.44

TR2-D2: Tree Search Guided Trajectory-Aware Fine-Tuning for Discrete Diffusion (2025)

Sophia Tang et al.

1.39

ActivityDiff: A diffusion model with Positive and Negative Activity Guidance for De Novo Drug Design (2025)

Renyi Zhou et al.

1.33

MODA: A Unified 3D Diffusion Framework for Multi-Task Target-Aware Molecular Generation (2025)

Dong Xu et al.

1.28

Unraveling the Potential of Diffusion Models in Small Molecule Generation (2025)

Peining Zhang et al.

1.28

MoDyGAN: Combining Molecular Dynamics With GANs to Investigate Protein Conformational Space (2025)

Jingbo Liang and Bruna Jacobson

1.28

LapDDPM: A Conditional Graph Diffusion Model for scRNA-seq Generation with Spectral Adversarial Perturbations (2025)

Lorenzo Bini et al.

1.22

Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings (2025)

Aditya Sengar et al.

1.22

A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization (2025)

Anjie Qiao et al.

1.17

CFP-Gen: Combinatorial Functional Protein Generation via Diffusion Language Models (2025)

Junbo Yin et al.

1.17

The Dance of Atoms-De Novo Protein Design with Diffusion Model (2025)

Yujie Qin et al.

1.11

NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation (2025)

Zhiyuan Liu et al.

1.00

Unified Guidance for Geometry-Conditioned Molecular Generation (2025)

Sirine Ayadi et al.

0.94

Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation (2024)

Can Xu et al.

—

Scalable Normalizing Flows Enable Boltzmann Generators for Macromolecules (2024)

Joseph C. Kim et al.

—

Autoregressive fragment-based diffusion for pocket-aware ligand design (2024)

Mahdi Ghorbani et al.

—

Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion (2024)

Alex Morehead et al.

—

Graph Diffusion Transformers for Multi-Conditional Molecular Generation (2024)

Gang Liu et al.

—

Dirichlet Flow Matching with Applications to DNA Sequence Design (2024)

Hannes Stark et al.

—

Text-Guided Molecule Generation with Diffusion Language Model (2024)

Haisong Gong et al.

—

Binding-Adaptive Diffusion Models for Structure-Based Drug Design (2024)

Zhilin Huang et al.

—

Diffusion on language model encodings for protein sequence generation (2024)

Viacheslav Meshchaninov et al.

—

3M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation (2024)

Huaisheng Zhu et al.

—

DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design (2024)

Jiaqi Guan et al.

—

DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization (2024)

Xiangxin Zhou et al.

—

Protein Conformation Generation via Force-Guided SE(3) Diffusion Models (2024)

Yan Wang et al.

—

Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization (2024)

Xiangxin Zhou et al.

—

Distributional Priors Guided Diffusion for Generating 3D Molecules in Low Data Regimes (2024)

Haokai Hong et al.

—

Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation (2024)

Ian Dunn et al.

—

De novo antibody design with SE(3) diffusion (2024)

Daniel Cutting et al.

—

BInD: Bond and Interaction-generating Diffusion Model for Multi-objective Structure-based Drug Design (2024)

Joongwon Lee et al.

—

RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching (2024)

Divya Nori et al.

—

Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules (2024)

Trevor Norton and Debswapna Bhattacharya

—

Improving Antibody Design with Force-Guided Sampling in Diffusion Models (2024)

Paulina Kulyt\.e et al.

—

General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design (2024)

Yue Jian et al.

—

Molecular Diffusion Models with Virtual Receptors (2024)

Matan Halfon et al.

—

Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization (2024)

Siyi Gu et al.

—

Repurformer: Transformers for Repurposing-Aware Molecule Generation (2024)

Changhun Lee et al.

—

Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design (2024)

Leo Klarner et al.

—

Training-Free Guidance for Discrete Diffusion Models for Molecular Generation (2024)

Thomas J. Kerby et al.

—

Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations (2024)

Sijia Wang et al.

—

BetterBodies: Reinforcement Learning guided Diffusion for Antibody Sequence Design (2024)

Yannick Vogt et al.

—

Text-guided Diffusion Model for 3D Molecule Generation (2024)

Yanchen Luo et al.

—

Pullback Flow Matching on Data Manifolds (2024)

Friso de Kruiff et al.

—

UniGEM: A Unified Approach to Generation and Property Prediction for Molecules (2024)

Shikun Feng et al.

—

Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation (2024)

Jiwoong Park et al.

—

Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design (2024)

Xiangxin Zhou et al.

—

E(3)-invariant diffusion model for pocket-aware peptide generation (2024)

Po-Yu Liang and Jun Bai

—

Awesome q-bio.BM

Datasets & benchmarks

Key papers

q-bio.BM

Awesome q-bio.BM

Datasets & benchmarks

Key papers