Ata uhi

I tiakina i:
Ngā taipitopito rārangi puna kōrero
Kaituhi matua: Gwozdz, Krzysztof
Hōputu: Recurso digital
Reo:
I whakaputaina: Zenodo 2026
Ngā marau:
protein dynamics
molecular dynamics
torsion angles
phase oscillators
neural ODE
Ramachandran
backbone reconstruction
NeRF
mdCATH
Timewarp
ml-for-biology
Urunga tuihono:https://doi.org/10.5281/zenodo.20100149
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Rārangi ihirangi:
  • 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.

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