AlphaDynamics: Compact Phase-Oscillator Neural Propagator for Protein Torsion Dynamics with Backbone 3D Reconstruction
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2026
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| _version_ | 1866902102224142336 |
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| author | Gwozdz, Krzysztof |
| author_facet | Gwozdz, Krzysztof |
| contents | AlphaDynamics v0.4.0 — Python package for predicting protein backbone torsion dynamics from sequence using a compact (78K params) phase-oscillator neural propagator. Achieves 2.39x lower mean Ramachandran JSD than Microsoft Timewarp 4AA model with 9,652x fewer parameters. New in v0.4.0: deterministic backbone 3D reconstruction from torsion trajectories using NeRF (Parsons 2005) with Engh-Huber 1991 standard bond geometry. Provides multi-model PDB output for visualization in PyMOL/VMD/ChimeraX, plus per-frame radius of gyration and end-to-end distance diagnostics. Scope note: best-validated for short peptides (4-15 aa); sequences longer than 20 aa are outside the calibrated scope. |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_20100149 |
| institution | Zenodo |
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| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | AlphaDynamics: Compact Phase-Oscillator Neural Propagator for Protein Torsion Dynamics with Backbone 3D Reconstruction Gwozdz, Krzysztof protein dynamics molecular dynamics torsion angles phase oscillators neural ODE Ramachandran backbone reconstruction NeRF mdCATH Timewarp ml-for-biology AlphaDynamics v0.4.0 — Python package for predicting protein backbone torsion dynamics from sequence using a compact (78K params) phase-oscillator neural propagator. Achieves 2.39x lower mean Ramachandran JSD than Microsoft Timewarp 4AA model with 9,652x fewer parameters. New in v0.4.0: deterministic backbone 3D reconstruction from torsion trajectories using NeRF (Parsons 2005) with Engh-Huber 1991 standard bond geometry. Provides multi-model PDB output for visualization in PyMOL/VMD/ChimeraX, plus per-frame radius of gyration and end-to-end distance diagnostics. Scope note: best-validated for short peptides (4-15 aa); sequences longer than 20 aa are outside the calibrated scope. |
| title | AlphaDynamics: Compact Phase-Oscillator Neural Propagator for Protein Torsion Dynamics with Backbone 3D Reconstruction |
| topic | protein dynamics molecular dynamics torsion angles phase oscillators neural ODE Ramachandran backbone reconstruction NeRF mdCATH Timewarp ml-for-biology |
| url | https://doi.org/10.5281/zenodo.20100149 |