The Open Free Energy toolkit

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

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

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

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

APBS - software for biomolecular electrostatics and solvation

Software for biomolecular electrostatics and solvation calculations

Analysis of non-covalent interactions in MD trajectories

A Python platform for Structural Bioinformatics

Python library for diffraction tomography with the Born and Rytov approximations

Modeling molecular ensembles with scalable data structures and parallel computing

a package to simulate fluid surfaces and biomembranes

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

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.

APBS & PDB2PQR - software for biomolecular electrostatics and solvation

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

Oil Palm Growth and Yield Model

A python library for advanced lattice light-sheet image analysis

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations

Robust and stable clustering of molecular dynamics simulation trajectories.

Collection of Python scripts to setup and run simulations with OpenMM

a Living ENsemble Simulator -- a lens to help you watch biophysics

Computational Biophysics for Medicine in 3D Slicer

A Python module intended to make cell segmentation, tracking and subsequent (mostly biophysical) statisticial analysis easy

genomics, biochemistry, biotechnology, cell biology, biophysics, ecology

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

Multi platform molecular dynamics simulator for coarse-grained MD simulation on GPU.

vertex model implementation to simulate biological tissue in 3D

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

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