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equidock_public

EquiDock: geometric deep learning for fast rigid 3D protein-protein docking

espaloma

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

gamd-openmm

Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers. http://miao.compbio.ku.edu/GaMD/

gibbs

Gibbs sampling for expanded ensembles and replica exchange simulations

glam

Code for "An adaptive graph learning method for automated molecular interactions and properties predictions".

gmt

Official Code Repository for the paper "Accurate Learning of Graph Representations with Graph Multiset Pooling" (ICLR 2021)

grand

A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.

graph-generation

GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models

graph-neural-networks

graph-transformer-pytorch

Implementation of Graph Transformer in Pytorch, for potential use in replicating Alphafold2

graphbp

Official implementation of "Generating 3D Molecules for Target Protein Binding"

graphit

Official Pytorch Implementation of GraphiT

gvp-pytorch

Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure

hgraph2graph

Hierarchical Generation of Molecular Graphs using Structural Motifs

hybrid_fep-ml

icml18-jtnn

Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)

jax-reaxff

JAX-ReaxFF: A Gradient Based Framework for Extremely Fast Optimization of Reactive Force Fields

jraph

A Graph Neural Network Library in Jax

keras2torch

lipophilicity-prediction

Code for "Lipophilicity Prediction with Multitask Learning and Molecular Substructures Representation" paper. Machine Learning for Molecules Workshop @ NeurIPS 2020

meld

Modeling with limited data

miniomm

A simple OpenMM wrapper for common-case MD runs

modof

Molecule Optimization via Fragment-based Generative Models

moleculex

nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

neurips19-graph-protein-design

Generative Models for Graph-Based Protein Design

openbpmd

OpenBPMD for MD_VS

openmm-atmmetaforce-plugin

An OpenMM plugin that implements the Alchemical Transfer Potential

openmm-cookbook

Proof-of-concept for the OpenMM Cookbook

openmm-pulling

Pulling Simulation and Smoothing