biophysics

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.

Software for biomolecular electrostatics and solvation calculations

APBS - software for biomolecular electrostatics and solvation

Analysis of non-covalent interactions in MD trajectories

Python library for diffraction tomography with the Born and Rytov approximations

A Python platform for Structural Bioinformatics

a package to simulate fluid surfaces and biomembranes

Modeling molecular ensembles with scalable data structures and parallel computing

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.

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

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

Open-source virtual microscope lab: real microorganisms, cell cultures and plant tissues whose life emerges from physics (soft bodies, low-Reynolds fluid, chemistry). Reproducible and measurable, for research and teaching.

A python library for advanced lattice light-sheet image analysis

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations