hale's repositories
mmpdb
A package to identify matched molecular pairs and use them to predict property changes.
matcher
Matcher is a tool for understanding how chemical structure optimization problems have been solved. Matcher enables deep control over searching structure/activity relationships (SAR) derived from large datasets, and takes the form of an accessible web application with simple deployment. Matcher is built around the mmpdb platform.
DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
RxnScribe
A Sequence Generation Model for Reaction Diagram Parsing
MolScribe
Robust Molecular Structure Recognition with Image-to-Graph Generation
Lomap
Alchemical mutation scoring map
BFEE2
binding free energy estimator 2
gnina
A deep learning framework for molecular docking
OpenNMT-py
Open Source Neural Machine Translation in PyTorch
DiffLinker
DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design
galaxy-tools-compchem
:mega: Galaxy Tools for Computational Chemistry
watvina
implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking
examples
A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.
MCMG
MCMG_V1
torchdrug
A powerful and flexible machine learning platform for drug discovery
OpenNMT-Tutorial
Neural Machine Translation (NMT) tutorial. Data preprocessing, model training, evaluation, and deployment.
DIG
A library for graph deep learning research
ChemTSv2
Refined and extended version of ChemTS
DiffSBDD
A Euclidean diffusion model for structure-based drug design.
Dock-MD-FEP
A three-in-one workflow, Dock with Autodock, MD with OpenMM, FEP with OpenMM/yank
3DLinker
An E(3) Equivariant Variational Autoencoder for Molecular Linker Design
DESERT
Zero-Shot 3D Drug Design by Sketching and Generating (NeurIPS 2022)
you-get
:arrow_double_down: Dumb downloader that scrapes the web
selfies
Robust representation of semantically constrained graphs, in particular for molecules in chemistry