Pinned Repositories
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
perses_jacs_systems
Prepared JACS systems for use with Perses and anything OpenMM
brycestx's Repositories
brycestx/perses_jacs_systems
Prepared JACS systems for use with Perses and anything OpenMM
brycestx/alchemical-analysis
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
brycestx/alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
brycestx/alchemlyb
the simple alchemistry library
brycestx/amber_rbfe_jacs
Amber relative binding free energy setup files for the JACS dataset
brycestx/deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
brycestx/dmm
Deep Markov Models
brycestx/edward
A library for probabilistic modeling, inference, and criticism. Deep generative models, variational inference. Runs on TensorFlow.
brycestx/FESetup
FESetup for automation of alchemical free energy simulation
brycestx/freenrgworkflows
Software for automated processing of alchemical free energy calculations
brycestx/learning_chem_trajectories
brycestx/Lomap
Alchemical mutation scoring map
brycestx/mdsrv
MD trajectory server
brycestx/msmbuilder
Statistical models for biomolecular dynamics
brycestx/nglview
IPython widget to interactively view molecular structures and trajectories
brycestx/openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
brycestx/openmmtools
An OpenMM toolkit with test systems, integrators, and alchemical support
brycestx/openmoltools
An open set of tools for automating tasks relating to small molecules
brycestx/perses
Experiments with expanded ensembles to explore chemical space
brycestx/pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR)
brycestx/pymc3
Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano
brycestx/pyro
Deep universal probabilistic programming with Python and PyTorch
brycestx/pytraj
Interactive data analysis for molecular dynamics simulations
brycestx/scikit-learn
scikit-learn: machine learning in Python
brycestx/Sire
Sire Molecular Simulations Framework
brycestx/soft-benchmarks
Soft benchmark sets for alchemical free energy calculations, for assessing their accuracy on biomolecular systems
brycestx/yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.