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Built on **JAX**, it provides auto-differentiable kernels to bridge structural ensembles and experimental protection factors.\n\n---\n\n## 🎯 Features\n\n- **Differentiable SASA Kernels:** Hardware-accelerated approximations of Solvent Accessible Surface Area using Gaussian occlusion models.\n- **Protection Factor Modeling:** Implementations of Linderstrøm-Lang models for H-exchange rates ($PF$).\n- **Kinetic Simulation:** Model time-dependent mass shifts using **EX2 kinetics** (Hvidt \u0026 Nielsen, 1966).\n- **Gradient-Based Refinement:** Optimize protein structures or ensembles directly against experimental HDX-MS time-curves.\n- **Vectorized Execution:** Native support for `vmap` to handle large conformational ensembles.\n\n---\n\n## 📚 Tutorials\n\nExperience **diff-hdx** directly in your browser:\n\n- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/elkins/diff-hdx/blob/main/examples/interactive_tutorials/hdx_prediction_tutorial.ipynb) **HDX-MS Prediction \u0026 Kinetics** — Learn how to simulate intrinsic rates, protection factors, and deuterium uptake curves.\n\n---\n\n## 🏗️ Technical Architecture\n\n- **Backend:** JAX (XLA-compiled) — supports CPU, GPU, and TPU.\n- **Differentiability:** Full support for forward and reverse-mode autodiff.\n- **Integration:** Compatible with `biotite` for structural parsing and `diff-biophys` for ensemble averaging.\n\n---\n\n## 🚀 Roadmap\n\n- [x] Initial differentiable SASA and $ln P$ kernels.\n- [x] Integration with JAX `vmap` for ensemble averaging.\n- [x] Residue-specific intrinsic exchange rates (Bai et al. 1993) — all 20 amino acids.\n- [ ] Integration with MD trajectory loaders.\n\n---\n\n## 🚀 Installation\n\n```bash\npip install diff-hdx\n```\n\n## 🧪 Scientific Validation\n\n- **Parity Checks:** Kernels are validated against standard non-differentiable implementations (e.g., `biotite` SASA) to ensure physical accuracy.\n- **Gradient Tests:** All kernels are verified using JAX's `gradcheck` to ensure numerically stable derivatives across the full support.\n- **Ensemble Consistency:** Verified against `diff-biophys` ensemble averaging for IDP conformational ensembles.\n\n---\n\n## 🔗 Related Projects\n\ndiff-hdx is part of the **differentiable biophysics** ecosystem:\n\n- [diff-biophys](https://github.com/elkins/diff-biophys) — Core differentiable biophysics engine.\n- [diff-fret](https://github.com/elkins/diff-fret) — Differentiable FRET modeling.\n- [diff-epr](https://github.com/elkins/diff-epr) — Differentiable EPR/DEER simulation.\n- [synth-pdb](https://github.com/elkins/synth-pdb) — Synthetic structure generation.\n\n---\n\n## 📖 Citation\n\n```bibtex\n@software{diff_hdx,\n  author  = {Elkins, George},\n  title   = {diff-hdx: Differentiable HDX-MS prediction in JAX},\n  year    = {2026},\n  url     = {https://github.com/elkins/diff-hdx},\n  version = {0.1.0}\n}\n```\n\n## ⚖️ License\n\nMIT\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Felkins-lab%2Fdiff-hdx","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Felkins-lab%2Fdiff-hdx","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Felkins-lab%2Fdiff-hdx/lists"}