Computational Biophysics Python Packages

bentopy

Packs stuff in boxes

synth-nmr

NMR spectroscopy calculations for protein structures. Jupyter Notebook tutorials are available to visualize the concepts.

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

diff-biophys

Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.

diff-hdx

Differentiable HDX-MS prediction in JAX

diff-fret

Differentiable FRET distance distribution modeling in JAX

diff-epr

Differentiable EPR/DEER distance distribution modeling in JAX

diff-em

Differentiable Cryo-EM map fitting in JAX

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.