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alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal

alchemlyb

the simple alchemistry library

amber_rbfe_jacs

Amber relative binding free energy setup files for the JACS dataset

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

dmm

Deep Markov Models

edward

A library for probabilistic modeling, inference, and criticism. Deep generative models, variational inference. Runs on TensorFlow.

fesetup

FESetup for automation of alchemical free energy simulation

freenrgworkflows

Software for automated processing of alchemical free energy calculations

learning_chem_trajectories

lomap

Alchemical mutation scoring map

mdsrv

MD trajectory server

msmbuilder

Statistical models for biomolecular dynamics

nglview

IPython widget to interactively view molecular structures and trajectories

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

openmmtools

An OpenMM toolkit with test systems, integrators, and alchemical support

openmoltools

An open set of tools for automating tasks relating to small molecules

perses

Experiments with expanded ensembles to explore chemical space

perses_jacs_systems

Prepared JACS systems for use with Perses and anything OpenMM

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

pymc3

Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano

pyro

Deep universal probabilistic programming with Python and PyTorch

pytraj

Interactive data analysis for molecular dynamics simulations

scikit-learn

scikit-learn: machine learning in Python

sire

Sire Molecular Simulations Framework

soft-benchmarks

Soft benchmark sets for alchemical free energy calculations, for assessing their accuracy on biomolecular systems

yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.