Biophysics Python Packages

mmcif-pdbx

Yet another version of PDBx/mmCIF Python implementation

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

diff-biophys

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

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..

nrefocus

python library for numerical focusing (refocusing, autofocusing) of complex wave fields

deeptrack

DeepTrack2 is a modular Python library for generating, manipulating, and analyzing image data pipelines for machine learning and experimental imaging.

acellera-pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

diff-em

Differentiable Cryo-EM map fitting in JAX

diff-epr

Differentiable EPR/DEER distance distribution modeling in JAX

diff-fret

Differentiable FRET distance distribution modeling in JAX

diff-hdx

Differentiable HDX-MS prediction in JAX

odtbrain

Python library for diffraction tomography with the Born and Rytov approximations

deerpredict

Software for the prediction of DEER and PRE data from conformational ensembles.

pyvertexmodel

3D vertex model allowing scutoids

synth-dynamics

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

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.

aims-immune

A software for the analysis of immune repertoires

polaritymodel

Code to investigate a polarity model of organ formation

pycapsid

A set of computational tools written in python for the analysis of viral capsids

domb-napari

napari plugin for analyzing fluorescence-labeled proteins redistribution

biskit

A Python platform for Structural Bioinformatics

papylio

Single-molecule fluorescence trace extraction and analysis

kif

KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.