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software-development
A primer on software development best practices for computational chemistryopenmmtools
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/2010.01196perses
Experiments with expanded ensembles to explore chemical spaceyank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.openmoltools
An open set of tools for automating tasks relating to small moleculesensembler
Automated omics-scale protein modeling and simulation setup.openmm-tutorials
Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMMmmtools
Some collected tools for molecular simulation pipelinesqmlify
espaloma_charge
Standalone charge assignment from Espaloma framework.ambermini
A stripped-down set of just antechamber, sqm, and tleap.gimlet
Graph Inference on MoLEcular Topologycpdetect
Change Point detectionneutromeratio
Tautomer ratios in solutionprotons
OpenMM testbed for constant-pH methodologies.thermopyl
Tools for ThermoML parsingasapdiscovery
Toolkit for open antiviral drug discovery by the ASAP Discovery Consortiumtorsionfit
Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.assaytools
Modeling and Bayesian analysis of fluorescence and absorbance assays.antibody-mutations
Assessing the impact of mutations on antibody-antigen binding affinityautomatic-equilibration-detection
Automatic detection of equilibrated regions of molecular simulationspymbar-examples
Examples of applications of pymbar to various problems in simulation and experimentpinot
Probabilistic Inference for NOvel Therapeuticschiron
Differentiable Markov Chain Monte Carlodrug-gym
Reinforcement learning environments for drug discoveryfeflow
Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkitsintegrator-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/e20050318yank-examples
Examples for use of YANK - getyank.orggibbs
Gibbs sampling for expanded ensembles and replica exchange simulationsmodelforge
Infrastructure to implement and train NNPskinase-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 paperalchemy
Alchemical tools for OpenMMcadd-grc-2013
Computer Aided Drug Discovery (CADD) GRC 2013 - slides, references, and examplesyank-benchmark
Standard experimental accuracy benchmark set for YANK.refit-espaloma
Refit espaloma with energies and forcesnano-drugbank
Cheminformatic analysis of small molecule type drugs in DrugBank for their ability to form nanoparticles with indocyanine dyes.sampl6-physicochemical-properties
SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)thresholds
Utilities for determining maximum tolerable timesteps. See https://doi.org/10.3390/e20050318fah-xchem
Tools and infrastructure for automated compound discovery using Folding@homecharge-datasets
AM1-BCC ELF10 small molecule training datasetsTargetExplorer
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 simulationautonomous-molecular-design
Sandbox for the development of active-learning algorithms for automated drug discovery.PDBfinder
a collection of scripts and files to help in PDB retrieval for various projectsmoldr
Manifold optimization for linear dimensionality reduction of MD trajectoriesSETD8-materials
Code and data for SETD8 simulationswetlab-protocols
A collection of protocols, primarily for automated protein expression and mutagenesismtenn
Modular Training and Evaluation of Neural Networksbayesian-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 contactsrobots
Laboratory automation toolkitsfah_prep
suite of functions to prepare simulations (docking, free energy) for use with folding at home.ROCSALT
Dual topology alchemical free energiesfahmunge
Tools for Munging Folding@Home datasetsalchemical-playground
Tutorials, examples, and thoughts on alchemical free energy calculationsopenmm7tutorials
Tutorials using new features in OpenMM 7Ligandr
Ligandr codefragmenter_data
Data for fragmenterring-open-fep
Ring-opening strategy for FEP.clusterutils
Utilities for running parallel jobs with Torque/Moab and MPIopenmm-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 domainsstatus
Ensembler2
resptools
Tools for multiconformer RESP fits using GAMESgbff
Tools for Bayesian forcefield developmentbellini
Bayesian Learning on Laboratory Investigationbrokenyank
YANK: GPU-accelerated calculation of ligand binding affinitiesdocker-fah-client
Information on running the Folding@Home client inside a docker imageSAMPL6-Reference-pKa-Calculations
Reference pKa calculations for the SAMPL6 pKa challengepymbar-datasets
oeante
Antechamber (AMBER GAFF parameterization engine) implementation using OpenEye toolstorsionfit_examples
examples and data for torsionfitfluorescence_assay_working_data
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 timesnn-endstates
MSMs
Markov state modelsinfiniteswitch
Implementation and testing of the infinite switch Hamiltonian exchange integrator.gcncharge
Graph convolutional networks for partial atomic chargeskinalysis
Scripts for analyzing simulations of kinases!papers-and-grants
YAML database of papers and grants from the Chodera labmsm-pipeline
A pipeline for MSMs.harbor
A home for docking evaluation and assessmentavoidome-analysis
A repository for downloading and analyzing the available Avoidome structuresERK-ancestral-materials
ERK ancestral reconstructionduke-cbb-talk-2014-10-06
Slides from John Chodera's CBB talk at Duke University on 6 Oct 2014assaytools2
Bayesian statistics-based assay modelling, accelerated by TensorFlow.enhanced-sampling-tmem175
Repository for running and assessing enhanced sampling simulations of TMEM175LDHA-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.OpenMMEnergyComparisons
Comparisons of energies and forces between OpenMM and other packageshsa-affinity
All Human Serum Albumin affinity measurements will be deposited here.octomore
finding eight or more parameters we can try for applying openpathsampling to kinaseskaizen
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