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ChemistryCheminformaticsCore Tools & Workflows

Core Tools & Workflows

Foundational cheminformatics tools, tutorials, and key molecular databases.

Tutorials & Courses Tools Datasets Awesome Lists Blogs

Tutorials

Practical Cheminformatics Jupyter / Colab
Fingerprints Clustering SAR Active learning
TeachOpenCADD T001-T010 Jupyter
Molecular data Fingerprints Similarity
RDKit Cookbook Documentation
RDKit fundamentals
Neural Networks for Chemists Jupyter
NN fundamentals Chemistry

Courses

AI4Chemistry Course
EPFL (CH-457) · Level: Graduate Covers molecular representations, GNNs, generative models, and reaction prediction.
Molecular representations GNNs Generative models Reaction prediction
Practical Programming in Chemistry
EPFL Introduction to programming for chemists: Python, Git, RDKit, data analysis workflows.
Python Git RDKit
Cheminformatics Teaching Material
Molecular representations, fingerprints, and computational methods.
Molecular representations Fingerprints

Tools

Core Cheminformatics Stack

RDKit Core toolkit — the foundation of most chemistry ML Datamol RDKit wrapper optimized for data science workflows OpenBabel Format conversion, 3D generation CDK Java-based toolkit Indigo Libraries and utilities cinfony Common API to cheminformatics toolkits SELFIES Self-Referencing Embedded Strings representation

Database Wrappers

PubChemPy Interact with PubChem in Python ChemSpiPy ChemSpider wrapper for searches chembl-downloader Automate downloading and querying ChEMBL NistChemPy NIST webbook data access

Visualization

nglview Jupyter widget to view molecular structures py3Dmol 3D molecular visualization in Jupyter mols2grid Interactive molecule grids chemiscope Interactive structure/property explorer

Datasets

MoleculeNet Comprehensive benchmark suite with multiple tasks TDC Therapeutics Data Commons — drug discovery datasets OCHEM 3.77M records for 689 chemical properties ChEMBL Bioactive molecules with drug-like properties PubChem Chemical information from 750+ data sources (116M compounds)

Awesome Lists

Tools & libraries  Python tools  ML-ready chemistry datasets  AI for chemistry papers  Drug discovery resources  Learning resources 

Blogs

The Valence Kjell Computational chemistry, ML Practical Cheminformatics Drug discovery, generative AI — Pat Walters Is Life Worth Living? Cheminformatics, RDKit — iwatobipen Byte Sized Chemistry Data viz, student perspective
CheminformaticsProperty Prediction & ADMET