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DeepTrackAI /DeepTrack2

Star217

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

machine-learning deep-learning image-processing optics microscopy data-augmentation biophysics soft-matter computational-pipelines photonics superresolution

UpdatedNov 5, 2025
Jupyter Notebook

OpenFreeEnergy /openfe

Star211

The Open Free Energy toolkit

molecular-dynamics computational-chemistry free-energy biophysics free-energy-calculations

UpdatedNov 5, 2025
Python

Electrostatics /pdb2pqr

Star156

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

bioinformatics chemistry help-wanted hacktoberfest biophysics

UpdatedMar 2, 2025
Python

drorlab /pensa

Star144

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

structural-biology molecular-dynamics biophysics biomolecules

UpdatedFeb 12, 2025
Python

Electrostatics /apbs-pdb2pqr

Star129

APBS - software for biomolecular electrostatics and solvation

bioinformatics chemistry biophysics

UpdatedJul 27, 2020

jaxleyverse /jaxley

Star123

Differentiable neuron simulations with biophysical detail on CPU, GPU, or TPU.

neuroscience biophysics jax hodgkin-huxley-model differentiable-simulations

UpdatedNov 5, 2025
Python

Electrostatics /apbs

Star115

Software for biomolecular electrostatics and solvation calculations

bioinformatics chemistry help-wanted hacktoberfest biophysics

UpdatedSep 7, 2024
C

maxscheurer /pycontact

Star64

Analysis of non-covalent interactions in MD trajectories

python bioinformatics chemistry analysis simulation toolkit dynamics molecular-structures molecular-dynamics computational-biology qt5 biochemistry interactions biophysics

UpdatedJan 3, 2025
Python

graik /biskit

Star57

A Python platform for Structural Bioinformatics

python bioinformatics scientific biophysics

UpdatedMar 18, 2025
Python

RI-imaging /ODTbrain

Star55

Python library for diffraction tomography with the Born and Rytov approximations

backpropagation biophysics diffraction-tomography single-cell-imaging

UpdatedMar 31, 2025
Python

bowman-lab /enspara

Star36

Modeling molecular ensembles with scalable data structures and parallel computing

python clustering protein-structure molecular-dynamics markov-state-model biophysics kinetic-modeling molecular-modeling

UpdatedOct 29, 2025
Python

weria-pezeshkian /FreeDTS

Star33

a package to simulate fluid surfaces and biomembranes

simulations surfaces biophysics membranes mesoscale

UpdatedAug 16, 2025
C++

kamerlinlab /KIF

Star31

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

machine-learning analysis proteins molecular-dynamics computational-biology interactions biophysics enzymes

UpdatedOct 31, 2025
Python

Electrostatics /electrostatics.github.io

Star30

APBS & PDB2PQR - software for biomolecular electrostatics and solvation

bioinformatics chemistry hacktoberfest biophysics

UpdatedJun 11, 2022
Python

martavarela /EP-PINNs

Star29

EP-PINNs implementation for 1D and 2D forward and inverse solvers for the Aliev-Panfilov cardiac electrophysiology model. Also includes Matlab finite-differences solver for data generation.

biophysics computational-model cardiac-electrophysiology physics-informed-neural-networks

UpdatedDec 7, 2022
MATLAB

osita-sunday-nnyigide /Pras_Server

Star28

Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by amide-amide interactions of the backbone

bioinformatics biophysics