biophysics

APBS - software for biomolecular electrostatics and solvation

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

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

A Python platform for Structural Bioinformatics

Software for biomolecular electrostatics and solvation calculations

The Open Free Energy toolkit

Analysis of non-covalent interactions in MD trajectories

Modeling molecular ensembles with scalable data structures and parallel computing

APBS & PDB2PQR - software for biomolecular electrostatics and solvation

Python library for diffraction tomography with the Born and Rytov approximations

A python library for advanced lattice light-sheet image analysis

Oil Palm Growth and Yield Model

Robust and stable clustering of molecular dynamics simulation trajectories.

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

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

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

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations

vertex model implementation to simulate biological tissue in 3D

Collection of Python scripts to setup and run simulations with OpenMM

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