choderalab/yank

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Language
Python
License
MIT License
Created about 11 years ago
Updated over 1 year ago

choderalab/yank

choderalab

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

YANK

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

Documentation

Documentation, tutorials, and best practices can be found at getyank.org.

Getting Started

See the Quickstart instructions.

Examples

Examples are available in the yank-examples repository:

git clone https://github.com/choderalab/yank-examples.git

Maintainers

Andrea Rizzi <[email protected]> (WCMC)
Hannah Bruce Macdonald <hannah.brucemacdonald> (MSKCC)
John D. Chodera <[email protected]> (MSKCC)
Levi N. Naden <[email protected]> (MSKCC)

Contributors

Kim Branson (Stanford)
Kyle A. Beauchamp (MSKCC)
Peter M. Eastman (Stanford)
Mark Friedrichs (Stanford)
Imran Haque (Stanford)
Patrick B. Grinaway (MSKCC)
Christoph Klein (University of Virginia)
Rosa Luirink (VU Amsterdam)
Daniel L. Parton (MSKCC)
Randy Radmer (Stanford)
Arien Sebastian Rustenburg (MSKCC)
Michael Shirts (University of Colorado Boulder)
Kai Wang (University of Virginia)

software-development

A primer on software development best practices for computational chemistry

openmmtools

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

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

perses

Experiments with expanded ensembles to explore chemical space

openmoltools

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

ensembler

Automated omics-scale protein modeling and simulation setup.

openmm-tutorials

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

Jupyter Notebook

mmtools

Some collected tools for molecular simulation pipelines

qmlify

Jupyter Notebook

espaloma_charge

Standalone charge assignment from Espaloma framework.

ambermini

A stripped-down set of just antechamber, sqm, and tleap.

gimlet

Graph Inference on MoLEcular Topology

cpdetect

Change Point detection

neutromeratio

Tautomer ratios in solution

Jupyter Notebook

protons

OpenMM testbed for constant-pH methodologies.

thermopyl

Tools for ThermoML parsing

asapdiscovery

Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium

torsionfit

Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.

Rich Text Format

assaytools

Modeling and Bayesian analysis of fluorescence and absorbance assays.

antibody-mutations

Assessing the impact of mutations on antibody-antigen binding affinity

automatic-equilibration-detection

Automatic detection of equilibrated regions of molecular simulations

pymbar-examples

Examples of applications of pymbar to various problems in simulation and experiment

pinot

Probabilistic Inference for NOvel Therapeutics

chiron

Differentiable Markov Chain Monte Carlo

drug-gym

Reinforcement learning environments for drug discovery

Jupyter Notebook

feflow

Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits

integrator-benchmark

Code for enumerating and evaluating numerical methods for Langevin dynamics using near-equilibrium estimates of the KL-divergence. Accompanies https://doi.org/10.3390/e20050318

Jupyter Notebook

yank-examples

Examples for use of YANK - getyank.org

gibbs

Gibbs sampling for expanded ensembles and replica exchange simulations

modelforge

Infrastructure to implement and train NNPs

kinase-metadynamics

To run metadynamics simulations using openMM (based on Peter Eastman's script)

perses-barnase-barstar-paper

Contains scripts and data for the perses barnase barstar paper

Jupyter Notebook

alchemy

Alchemical tools for OpenMM

cadd-grc-2013

Computer Aided Drug Discovery (CADD) GRC 2013 - slides, references, and examples

Jupyter Notebook

yank-benchmark

Standard experimental accuracy benchmark set for YANK.

Jupyter Notebook

refit-espaloma

Refit espaloma with energies and forces

nano-drugbank

Cheminformatic analysis of small molecule type drugs in DrugBank for their ability to form nanoparticles with indocyanine dyes.

Jupyter Notebook

sampl6-physicochemical-properties

SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)

Jupyter Notebook

thresholds

Utilities for determining maximum tolerable timesteps. See https://doi.org/10.3390/e20050318

fah-xchem

Tools and infrastructure for automated compound discovery using Folding@home

charge-datasets

AM1-BCC ELF10 small molecule training datasets

TargetExplorer

Database framework with RESTful API for aggregating genomic, structural, and functional data for target protein families.

saltswap

Package to fluctuate the number of counterions in an OpenMM simulation

Jupyter Notebook

autonomous-molecular-design

Sandbox for the development of active-learning algorithms for automated drug discovery.

Jupyter Notebook

PDBfinder

a collection of scripts and files to help in PDB retrieval for various projects

moldr

Manifold optimization for linear dimensionality reduction of MD trajectories

SETD8-materials

Code and data for SETD8 simulations

Jupyter Notebook

wetlab-protocols

A collection of protocols, primarily for automated protein expression and mutagenesis

mtenn

Modular Training and Evaluation of Neural Networks

bayesian-itc

Python tools for the analysis and modeling of isothermal titration calorimetry (ITC) experiments.

rbd-ace2-contact-analysis

Code and workflow for running MD simulations on Folding@home to analyze RBD:ACE2 contacts

robots

Laboratory automation toolkits

fah_prep

suite of functions to prepare simulations (docking, free energy) for use with folding at home.

ROCSALT

Dual topology alchemical free energies

fahmunge

Tools for Munging Folding@Home datasets

alchemical-playground

Tutorials, examples, and thoughts on alchemical free energy calculations

openmm7tutorials

Tutorials using new features in OpenMM 7

Ligandr

fragmenter_data

Data for fragmenter

Jupyter Notebook

ring-open-fep

Ring-opening strategy for FEP.

clusterutils

Utilities for running parallel jobs with Torque/Moab and MPI

openmm-validation

[Work in progress] An extensive validation suite for the OpenMM molecular simulation library.

pdbbind_ml

Scripts to train and evaluate ML models on the PDBBind dataset.

peptide-design

Design selective peptides targeting SH2 domains

Jupyter Notebook

status

Ensembler2

resptools

Tools for multiconformer RESP fits using GAMES

gbff

Tools for Bayesian forcefield development

bellini

Bayesian Learning on Laboratory Investigation

brokenyank

YANK: GPU-accelerated calculation of ligand binding affinities

docker-fah-client

Information on running the Folding@Home client inside a docker image

SAMPL6-Reference-pKa-Calculations

Reference pKa calculations for the SAMPL6 pKa challenge

Jupyter Notebook

pymbar-datasets

oeante

Antechamber (AMBER GAFF parameterization engine) implementation using OpenEye tools

torsionfit_examples

examples and data for torsionfit

Jupyter Notebook

fluorescence_assay_working_data

Jupyter Notebook

itctools

Tools for setting up ITC experiments in an automated fashion using the Tecan EVO and Auto-iTC 200.

mpiplus

Utilities to run on MPI.

msm-mfpt

Evaluating MSM-estimated mean first passage times

Jupyter Notebook

nn-endstates

Jupyter Notebook

DDR1_and_kinase_promiscuity_materials

Code and data for the paper 'What makes a kinase promiscuous for inhibitors?'.

Jupyter Notebook

MSMs

Markov state models

Jupyter Notebook

infiniteswitch

Implementation and testing of the infinite switch Hamiltonian exchange integrator.

gcncharge

Graph convolutional networks for partial atomic charges

Jupyter Notebook

kinalysis

Scripts for analyzing simulations of kinases!

papers-and-grants

YAML database of papers and grants from the Chodera lab

msm-pipeline

A pipeline for MSMs.

harbor

A home for docking evaluation and assessment

avoidome-analysis

A repository for downloading and analyzing the available Avoidome structures

Jupyter Notebook

ERK-ancestral-materials

ERK ancestral reconstruction

Jupyter Notebook

duke-cbb-talk-2014-10-06

Slides from John Chodera's CBB talk at Duke University on 6 Oct 2014

assaytools2

Bayesian statistics-based assay modelling, accelerated by TensorFlow.

Jupyter Notebook

enhanced-sampling-tmem175

Repository for running and assessing enhanced sampling simulations of TMEM175

Jupyter Notebook

LDHA-MCCE

MCCE2 calculations for Lactate dehydrogenase A (collaboration with Thompson lab and Gunner lab)

IR783-QSNAP

Analysis of Quantitative Structure-Nanoparticle Assembly Prediction (QSNAP) descriptors for predicting drug-indocyanine dye (IR783) nanoparticle formation.

Jupyter Notebook

OpenMMEnergyComparisons

Comparisons of energies and forces between OpenMM and other packages

hsa-affinity

All Human Serum Albumin affinity measurements will be deposited here.

Jupyter Notebook

octomore

finding eight or more parameters we can try for applying openpathsampling to kinases

Jupyter Notebook

kaizen

Continual improvement