Popular GitHub Repositories for Cheminformatics

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

Python package for graph neural networks in chemistry and biology

A tool for retrosynthetic planning

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

Deep Reinforcement Learning for de-novo Drug Design

Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.

Experimental design and (multi-objective) bayesian optimization.

ANI-1 neural net potential with python interface (ASE)

Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology

The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.

Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.

SELFormer: Molecular Representation Learning via SELFIES Language Models

A web app and Python API for multi-modal RAG framework to ground LLMs on high-fidelity materials informatics. An agentic materials scientist powered by @materialsproject, @langchain-ai, and @openai

A library to interface molecules and machine learning.

Graph neural networks for molecular machine learning. Implemented and compatible with TensorFlow and Keras.

organic chemistry reaction prediction using NMT with Attention

Automated machine learning protocols that start from CSV databases of descriptors or SMILES and produce publication-quality results in Chemistry studies with only one command line.

LLM Agent that leverages cheminformatics tools to provide informed responses.

(differentiable) gradient-based optimization on a chemical graph for de novo molecule design/optimization (ICLR 2022)

Amons-based quantum machine learning for quantum chemistry