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.

jaxfne

Tensor-Field Neural Equations (TFNE) in JAX

deeptrack

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

proteuspy

A package for the modeling and analysis of proteins of known structure

acellera-pdb2pqr

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

odtbrain

Python library for diffraction tomography with the Born and Rytov approximations

synth-nmr

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

pycapsid

Python package to extract quasi-rigid domains in protein shells and other macromolecular complexes.

deerpredict

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

aims-immune

AIMS - Automated Immune Molecule Separator: An analysis pipeline for distinguishing distinct subsets of Ig and MHC molecules. See below site for documentation

nrefocus

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

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..

domb-napari

napari plugin for analyzing fluorescence-labeled proteins redistribution

papylio

Single-molecule fluorescence trace extraction and analysis

biskit

A Python platform for Structural Bioinformatics

mcp-pykingenie

MCP_PYKINGENIE is a MCP server that provides tools for the analysis of surface-based binding kinetics data.

kif

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

pensa

PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.

pysawit

Oil Palm Growth and Yield Model

diff-biophys

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

kryptorious-qbio-coherence

NULLIUS: an adversarial truth ledger for biological quantum-coherence claims, anchored to the Firmenich 2026 HEOM dephasing baseline.

bimato

A library containing all the biopolymer matrix topology analyses published by the Biological Physics Group, (BIP), Peter Debye Institute, University Leipzig.

diff-hdx

Differentiable HDX-MS prediction in JAX