BoltzGen is a deep learning pipeline for computational protein and peptide binder design. It provides a command-line interface (boltzgen) that orchestrates a multi-step workflow: diffusion-based backbone generation, inverse folding (sequence design given structure), folding with Boltz-2, affinity prediction, analysis, and filtering/ranking of designs. The system supports diverse protocols including protein, peptide, nanobody, antibody, and small-molecule targeting, with extensive conditioning options like binding sites, disulfide bonds, cyclization, and per-residue constraints. The codebase is structured as a Python package with modular components for data parsing (YAML design specs, mmCIF/PDB), featurization, tokenization, cropping, and model layers (pairformer, attention, diffusion, inverse folding). It includes training pipelines with Hydra configuration, PyTorch Lightning, and validation splits. While primarily an application, it also contains research-grade example datasets and a Jupyter notebook for filtering, reflecting its origin in a bioRxiv publication. The architecture is well-organized but shows some technical drift (hardcoded paths, print statements, broad exception handling) and dependency on specific CUDA versions.
This repository is a curated, comprehensive list of academic papers on the application of deep learning to protein design. It is not a software application or a data pipeline; rather, it is a living bibliography organized by research area (e.g., inverse folding, diffusion-based design, language models, antibody design). The README.md file contains hundreds of paper entries with links to publications, code repositories, and supplementary materials, updated frequently (last update shown as 2026.08.02). There is no executable code, no datasets, and no computational workflows. The value lies in its role as a reference index for researchers and practitioners tracking the rapidly evolving field of AI-driven protein design.