Protein Dynamics Python Packages

makeshift-nmr

open-source python package for accessing and analyzing NMR data

alphadynamics

Compact sequence-only neural propagator for protein torsion dynamics. 2.39x lower JSD than Microsoft Timewarp at 3000x fewer parameters. pip install alphadynamics.

pyhdx

Derive ΔG for single residues from HDX-MS data

sinatra-pro

Topological data analytic approach for discovering biophysical signatures in protein dynamics

synth-afm

Differentiable High-Speed AFM (HS-AFM) simulation for protein structures. JAX-powered toolkit for generating synthetic movies with realistic tip-dilation and scanning lag.

synth-dynamics

Fast Langevin dynamics engine using the Anisotropic Network Model (ANM) for rapid protein conformational ensemble generation.