{"id":50730861,"url":"https://github.com/elkins/diff-hdx","last_synced_at":"2026-06-10T08:31:52.704Z","repository":{"id":362584871,"uuid":"1259836276","full_name":"elkins/diff-hdx","owner":"elkins","description":"Differentiable HDX-MS prediction in JAX","archived":false,"fork":false,"pushed_at":"2026-06-04T23:58:53.000Z","size":629,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-06-05T01:05:18.530Z","etag":null,"topics":["biophysics","differentiable-programming","hdx-ms","jax","structural-biology"],"latest_commit_sha":null,"homepage":"https://elkins.github.io/diff-hdx/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/elkins.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-06-04T23:00:49.000Z","updated_at":"2026-06-04T23:59:37.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/elkins/diff-hdx","commit_stats":null,"previous_names":["elkins/diff-hdx"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/elkins/diff-hdx","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/elkins%2Fdiff-hdx","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/elkins%2Fdiff-hdx/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/elkins%2Fdiff-hdx/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/elkins%2Fdiff-hdx/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/elkins","download_url":"https://codeload.github.com/elkins/diff-hdx/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/elkins%2Fdiff-hdx/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34144679,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-10T02:00:07.152Z","response_time":89,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biophysics","differentiable-programming","hdx-ms","jax","structural-biology"],"created_at":"2026-06-10T08:31:52.039Z","updated_at":"2026-06-10T08:31:52.692Z","avatar_url":"https://github.com/elkins.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 🧪 diff-hdx: Differentiable HDX-MS Prediction in JAX\n\n[![Tests](https://github.com/elkins/diff-hdx/actions/workflows/test.yml/badge.svg)](https://github.com/elkins/diff-hdx/actions/workflows/test.yml)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![JAX](https://img.shields.io/badge/backend-JAX-9cf.svg)](https://github.com/google/jax)\n\n**diff-hdx** is a high-performance Python library for differentiable Hydrogen-Deuterium Exchange (HDX-MS) prediction. 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## 🏗️ 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%2Fdiff-hdx","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Felkins%2Fdiff-hdx","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Felkins%2Fdiff-hdx/lists"}