The Open Free Energy toolkit

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.

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

A Python platform for Structural Bioinformatics

Analysis of non-covalent interactions in MD trajectories

Python library for diffraction tomography with the Born and Rytov approximations

Modeling molecular ensembles with scalable data structures and parallel computing

APBS & PDB2PQR - software for biomolecular electrostatics and solvation

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

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

Collection of Python scripts to setup and run simulations with OpenMM

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations

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

Computational Biophysics for Medicine in 3D Slicer

A Python package to conduct 3D Traction Force Microscopy on multicellular aggregates (spheroids).

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

Yet another version of PDBx/mmCIF Python implementation

DeepDriveMD implemented with Colmena