IAlibay

hamilton

Hamilton helps data scientists and engineers define testable, modular, self-documenting dataflows, that encode lineage and metadata. Runs and scales everywhere python does.

dmol-book

Deep learning for molecules and materials book

AutoDock-Vina

AutoDock Vina

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

perses

Experiments with expanded ensembles to explore chemical space

All-In

"Open sourcing Diversity and Inclusion."

openfe

The Open Free Energy toolkit

soc-viz-of-the-week

Son of a Corner's viz of the week

spin

Developer tool for scientific Python libraries

WorkshopMDMLEdinburgh2022

gnina-torch

🔥 PyTorch implementation of GNINA scoring function for molecular docking

handbook

The Contributor Experience Handbook

WorkshopPrace2021

Materials for the 2021 PRACE Workshop @ SurfSARA

membrane-curvature

MDAnalysis tool to calculate membrane curvature.

gufe

grand unified free energy by OpenFE

pKAI

pKAI: a fast and interpretable deep learning approach to accurate electrostatics-driven pKa prediction

alchemiscale

a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home

X-Entropy

This package is meant to calculate the dihedral entropy of a biomolecule. However, it can also calculate the entropy of any binnable data or simply the KDE of that data.

kartograf

This is an package contains tools for setting up hybrid-topology FE calculations

MDAnalysis.github.io

MDAnalysis home page mdanalysis.org as GitHub pages.

infrastructure

Policies, Configurations, and Documentation of NumFOCUS Managed Infrastructure

molstarview

Try to bring molstar to Jupyter notebook (no lab yet).

abfe-benchmark

cookiecutter-mdakit

Cookiecutter for Python packages based on MDAnalysis

mdahole2

An MDAKit implementing a Python interface for the HOLE program.

openfe_skunkworks

experimental toybox

md2stl

mdanalysis-sphinx-theme

The official MDAnalysis Sphinx documentation theme.

ofe-sphinx-theme

Sphinx theme for Open Free Energy software based on the PyData theme.

openfreeenergy.github.io