Find open-source science resources

All-atom biomolecular structure prediction for protein-nucleic acid-small molecule-metal ion complexes, enabling accurate modeling of covalent modifications and assemblies beyond proteins (Baker Lab, Science 2024)

Baidu's open-source reproduction of AlphaFold3 in PaddlePaddle, providing pretrained weights and inference pipelines for unified biomolecular structure prediction across proteins, nucleic acids, ligands, ions, and post-translational modifications within the PaddleHelix biocomputing platform (Baidu, bioRxiv 2024)

Trainable PyTorch reproduction of AlphaFold 3

Fully open-source (Apache 2.0) biomolecular structure prediction reproducing AlphaFold3, free for academic and commercial use (Columbia AlQuraishi Lab & OpenFold Consortium, 2025)

Trainable, memory-efficient PyTorch reproduction and retraining of AlphaFold2 providing new insights into its learning dynamics and out-of-distribution generalization; widely used as the open-source AlphaFold2 backbone underpinning many downstream protein structure prediction and design pipelines (Columbia AlQuraishi Lab & OpenFold Consortium, Nature Methods 2024)

AlphaFold/ESMFold accessible implementation with AF3 JSON export, database updates

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)

AlphaFold 3 inference pipeline for unified biomolecular structure prediction of proteins, nucleic acids, small molecules, ions, and post-translational modifications (Google DeepMind, Nature 2024)

Protein structure prediction

Neural network-based cryo-EM heterogeneous reconstruction, modeling continuous 3D structure distributions from single-particle images, with CryoDRGN-ET extending to in-cell cryo-electron tomography (MIT CSAIL, Nature Methods 2021/2024)