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Graph neural network operating entirely at the atomic level for protein-ligand conformational ensemble prediction and docking, generating diverse solutions through rapid stochastic denoising to model conformational heterogeneity (Baker Lab, bioRxiv 2025)

Discovering interpretable features in protein language models via sparse autoencoders, enabling mechanistic understanding of PLM representations for protein engineering and design (288+ stars, MIT License)

State-specific protein-ligand complex structure prediction with a multi-scale deep generative model, enabling conformational state-aware modeling of molecular interactions (329+ stars, 2024)

AI-assisted mutation nomination approach optimizing protein function by integrating structural and evolutionary constraints into protein inverse folding models, compatible with ProteinMPNN, LigandMPNN, ESM-IF1, and SaProt (Chinese Academy of Sciences, 359+ stars)

Partially latent flow matching model for the joint generation of a protein's amino acid sequence and full atomistic structure, including both backbone and side chains (2025)

Dynamic Protein Data Bank integrating dynamic behaviors and physical properties into protein structures via a new dataset and SE(3) model extension, enabling richer understanding of protein conformational landscapes (Fudan University, 784+ stars)

Family of diffusion protein language models demonstrating versatile generative and predictive capabilities for protein sequences and structures, including multimodal co-generation, conditional folding, inverse folding, motif scaffolding, and representation learning, with open pretrained weights and training scripts (327+ stars, ICML 2024, ICLR 2025, ICML 2025 Spotlight)

Large-scale flow-based protein backbone generator utilizing hierarchical fold class labels for conditioning with a tailored scalable transformer architecture, enabling controllable de novo protein design (264+ stars)

Public release of Profluent's ProGen3 protein language model family, including PMC-15B supporting sequence- and structure-conditioned generation for protein design, zero-shot fitness prediction, and antibody engineering with state-of-the-art performance on fitness and docking benchmarks (114+ stars, Apache 2.0)

In silico directed evolution framework using few-shot active learning to optimize protein activities, enabling rapid protein engineering with minimal experimental data (352+ stars, 2023)

Universal 3D molecular pretraining framework with 209M conformations, scaling to 1.1B parameters (Uni-Mol2) on 800M conformations for molecular property prediction, docking, and quantum chemistry (ICLR 2023, NeurIPS 2024)

State-of-the-art pretrained language models for proteins trained on thousands of GPUs and Google TPUs using Transformer architectures, enabling protein property prediction, feature extraction, and transfer learning across diverse downstream tasks (1.3K+ stars, MIT, 2020-2026)

Diffusion-based molecular docking achieving SOTA blind docking performance, treating ligand pose prediction as generative diffusion over SE(3), with DiffDock-L update for improved generalization (MIT CSAIL, ICLR 2023)

LLM-based molecular optimization tool

Extension of ProteinMPNN for protein sequence design in the context of small-molecule ligands, metal ions, and nucleic acids, enabling binding site engineering and co-factor redesign (Baker Lab)

Large-scale biomolecular instruction dataset for chemistry/biology LLMs (ICLR2024)

Chemical language model

Deep learning-based protein sequence design (inverse folding) from backbone structures, achieving 52.4% sequence recovery vs 32.9% for Rosetta, core tool in modern protein design pipelines (Baker Lab, Science 2022)

Powerful and flexible machine learning platform for drug discovery, providing comprehensive tools for molecular property prediction, generative models, knowledge graph reasoning, and reaction prediction with PyTorch backend (1.5K+ stars)

Diffusion model for scalable protein structure design with multi-motif scaffolding capabilities, achieving state-of-the-art designability, diversity, and novelty through SE(3)-equivariant attention and massive data augmentation (AlQuraishi Lab, 2024)

Generative model for programmable protein design using diffusion modeling, equivariant graph neural networks, and conditional random fields to efficiently sample diverse all-atom structures; supports conditional generation via composable conditioners for substructure, symmetry, shape, and neural-network predictions; validated crystallographically (Generate Biomedicines, Nature 2023)

3D Equivariant Diffusion for Target-Aware Molecule Generation (ICLR2023)

Deep learning system for de novo design of high-affinity protein binders, achieving strong binding across diverse target classes including challenging intracellular proteins with significantly higher success rates than traditional wet-lab screening methods (Google DeepMind, Nature 2024)