Browse community-submitted repositories with citations, contributors, and links back to the original project.
105 approved code entries are available for search indexing and community discovery.
MACE foundation models (MP, OMAT, mh-1) Why it is useful: Molecular simulation and atomistic ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 266 stars, 25 fork...
HTMD: Programming Environment for Molecular Discovery Why it is useful: Molecular simulation and atomistic ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 274...
MoleculeKit: Your favorite molecule manipulation kit Why it is useful: Molecular simulation and atomistic ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 237 s...
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results. Why it is useful: Docking and protein-ligand modeling repositor...
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022) Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows...
Working with molecular structures in pandas DataFrames Why it is useful: Chemistry software and utilities repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 752 star...
A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization. (Nature CommsChem) Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthe...
De Novo Drug Design with RNNs and Transformers Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 186 stars, 29 forks,...
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL) Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discover...
Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al. Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecul...
A powerful and flexible machine learning platform for drug discovery Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals:...
Mixed continous/categorical flow-matching model for de novo molecule generation. Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. Git...
Official repository for MolCRAFT series Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 155 stars, 11 forks, primary...
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulati...
BoltzGen: Toward Universal Binder Design Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 971 stars, 240 fork...
A C++ library for efficient tensor network calculations Why it is useful: Chemistry software and utilities repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 403 sta...
Scikit-learn compatible library for molecular fingerprints and chemoinformatics Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. G...
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows....
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022). Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug...
Geometric Latent Diffusion Models for 3D Molecule Generation Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 277 sta...
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization. Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation,...
A tool for retrosynthetic planning Why it is useful: Reaction informatics and synthesis repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 847 stars, 178 forks, prim...
An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular design Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular M...
BioNeMo Framework: For building and adapting AI models in drug discovery at scale Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. Gi...
GenMol is a generative AI model for creating novel molecules. It utilizes masked discrete diffusion and fragment-based generation to create valid molecules, which are encoded in the SAFE molecular representation. Why it is useful: Generati...
A high-performance, GPU-accelerated library for key computational chemistry tasks, such as molecular similarity, conformer generation, and geometry relaxation. Why it is useful: Chemistry software and utilities repository for chemistry, ch...
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Why it is useful: Drug discovery and ADMET ML repository for che...
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Why it is useful: Drug discovery and ADMET ML...
Manipulating VASP files with Python. Why it is useful: Materials and crystal chemistry repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 300 stars, 96 forks, primar...
quacc is a flexible platform for computational materials science and quantum chemistry that is built for the big data era. Why it is useful: Quantum chemistry and simulation repository for chemistry, cheminformatics, molecular ML, simulati...
Python version of the amazing Reaction Mechanism Generator (RMG). Why it is useful: Reaction informatics and synthesis repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub sign...
This repo contains the codes for our paper: Molecule Generation by Principal Subgraph Mining and Assembling. Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or d...
Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug...
[ICML 2024] Interaction-based Retrieval-augmented Diffusion Models for Protein-specific 3D Molecule Generation Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or...
Protein Graph Library Why it is useful: Chemistry software and utilities repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 1174 stars, 141 forks, primary language:...
Source code for ICLR2025 paper "NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation". Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or...
[ICLR 2023 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs Why it is useful: Molecular simulation and atomistic ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or dr...
[ICLR 2024] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations Why it is useful: Molecular simulation and atomistic ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis,...
Python package for graph neural networks in chemistry and biology Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 80...
⚗ A package useful for chemistry written in Python Why it is useful: Reaction informatics and synthesis repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 647 stars,...
[Briefings In Bioinformatics] DrugAssist: A Large Language Model for Molecule Optimization Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery work...
Interactive molecule viewer for 2D structures Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 254 stars, 34 forks...
The Chemistry Development Kit Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 585 stars, 175 forks, primary langu...
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signa...
Multi-modal Molecule Structure-text Model for Text-based Editing and Retrieval, Nat Mach Intell 2023 (https://www.nature.com/articles/s42256-023-00759-6) Why it is useful: Chemistry software and utilities repository for chemistry, cheminfo...
Official Python client for accessing ChEMBL API Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 444 stars, 103 fo...
Interaction Fingerprints for protein-ligand complexes and more Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signal...
Message Passing Neural Networks for Molecule Property Prediction Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 238...
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals:...
Molecular Processing Made Easy. Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 537 stars, 62 forks, primary lang...
A single model for all your molecular design tasks Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 181 stars, 20 for...
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology Why it is useful: Quantum chemistry and simulation repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug dis...
Universal cheminformatics toolkit, utilities and database search tools Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub sig...
Web-based molecule sketcher Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 810 stars, 242 forks, primary languag...
The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research. Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discov...
Experimental design and (multi-objective) bayesian optimization. Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals:...
Interface for AutoDock, molecule parameterization Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 371 stars, 72 fork...
Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022) Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflo...
[ICLR 2022] Data-Efficient Graph Grammar Learning for Molecular Generation Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub si...
A deep learning framework for molecular docking Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 935 stars, 1...
The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023) Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulat...
Deep Reinforcement Learning for de-novo Drug Design Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 369 stars, 13...
Interactive browser visualizations for materials science: crystal structures/molecules, trajectories, convex hulls, phase diagrams, Fermi surfaces, bands+DOS, Brillouin zones, etc. Why it is useful: Materials and crystal chemistry reposito...
Tensorflow + Molecules = TensorMol Why it is useful: Molecular simulation and atomistic ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 277 stars, 73 forks, pr...
Official repository for the Boltz biomolecular interaction models Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub sig...
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics) Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or...
Open-source chemistry software repository. Why it is useful: Materials and crystal chemistry repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 259 stars, 42 forks,...
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug dis...
The code for "Graph Diffusion Transformer for Multi-Conditional Molecular Generation" Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows...
A python package for accessing various properties of elements, ions and isotopes in the periodic table of elements. Why it is useful: Materials and crystal chemistry repository for chemistry, cheminformatics, molecular ML, simulation, synt...
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases. Why it is useful: Generative molecular design repository for chemistry, chemin...
Deep generative models of 3D grids for structure-based drug discovery Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals...
Automatically extract chemical information from scientific documents Why it is useful: Chemistry software and utilities repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub sig...
Python wrapper for the PubChem PUG REST API. Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 504 stars, 121 forks...
Implementation of MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or...
Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub sig...
TxGNN: Zero-shot prediction of therapeutic use with geometric deep learning and clinician centered design Why it is useful: Drug discovery and ADMET ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug...
Allegro is a code for building highly scalable E(3)-equivariant interatomic potentials Why it is useful: Molecular simulation and atomistic ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discover...
NequIP is a code for building E(3)-equivariant interatomic potentials Why it is useful: Molecular simulation and atomistic ML repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitH...
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitH...
NWChem: Open Source High-Performance Computational Chemistry Why it is useful: Quantum chemistry and simulation repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 60...
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows....
Open Drug Discovery Toolkit Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 464 stars, 124 forks, primary la...
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery work...
A Javascript cheminformatics toolkit. Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 276 stars, 67 forks, primar...
Atomsk: A Tool For Manipulating And Converting Atomic Data Files - Why it is useful: Quantum chemistry and simulation repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signa...
PhoreGen: Pharmacophore-Oriented 3D Molecular Generation towards Efficient Feature-Customized Drug Discovery https://www.nature.com/articles/s43588-025-00850-5 Why it is useful: Generative molecular design repository for chemistry, cheminf...
Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python Why it is useful: Quantum chemistry and simulation repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery wo...
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning. Why it is useful: Docking and protein-ligand modeling repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug...
The official sources for the RDKit library Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 3465 stars, 1021 forks...
A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit . Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discover...
A small, highly performant JavaScript component for parsing and drawing SMILES strings. Released under the MIT license. Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, s...
RXNMapper: Unsupervised attention-guided atom-mapping. Code complementing our Science Advances publication on "Extraction of organic chemistry grammar from unsupervised learning of chemical reactions" (https://advances.sciencemag.org/conte...
SpectroChemPy is a framework for processing, analyzing and modeling spectroscopic data for chemistry with Python Why it is useful: Spectra and analytical chemistry repository for chemistry, cheminformatics, molecular ML, simulation, synthe...
Robust Molecular Structure Recognition with Image-to-Graph Generation Why it is useful: Chemistry software and utilities repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub si...
Hierarchical Generation of Molecular Graphs using Structural Motifs Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals:...
Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018) Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. Git...
add-on to plotly which show molecule images on mouseover! Why it is useful: Cheminformatics infrastructure repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signals: 263 sta...
Implementation of ICLR23 paper "Molecule Generation for Target Protein Binding with Structural Motifs" Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug di...
[ICLR 2024] Domain-Agnostic Molecular Generation with Chemical Feedback Why it is useful: Generative molecular design repository for chemistry, cheminformatics, molecular ML, simulation, synthesis, or drug discovery workflows. GitHub signa...
A curated list of efforts in materials informatics, bridging materials science, computer science, and data science.
The BOSS (Bayesian Optimization for Surface Science) project aims to develop and implement Bayesian optimization techniques for accelerating materials discovery and design in surface science.
The Atomic Simulation Environment (ASE) is a Python package that provides a convenient framework for setting up, running, and analyzing atomic simulations. It supports a wide range of calculators and offers tools for structure optimization...
Best of Atomistic Machine Learning - curated list with 510+ atomistic projects Contents - Active learning _9 projects_ - Community resources _38 projects_ - Datasets _55 projects_ - Data Structures _4 projects_ - Density functional theory...
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