Cheminformatics

This skill provides comprehensive documentation and guidance for using datamol, a Python library that simplifies molecular cheminformatics tasks. It covers SMILES parsing, molecular descriptors, fingerprints, clustering, 3D conformer generation, visualization, and chemical reactions with sensible defaults built on top of RDKit.

This skill enables querying the PubChem database, the world's largest freely available chemical database with 110M+ compounds. It supports searching compounds by name, structure (SMILES/InChI), or formula, retrieving molecular properties, performing similarity and substructure searches, and accessing bioactivity data from screening assays.

This skill enables querying the ChEMBL database, a manually curated collection of over 2 million bioactive molecules maintained by the European Bioinformatics Institute. It supports compound searches, target information retrieval, bioactivity data queries (IC50, Ki, EC50), similarity/substructure searches, and drug discovery workflows for medicinal chemistry research.

TorchDrug is a documentation skill that provides comprehensive guidance for using the TorchDrug PyTorch library in drug discovery and molecular science. It covers graph neural networks for molecules and proteins, including molecular property prediction, protein modeling, knowledge graph reasoning, molecular generation, and retrosynthesis planning with 40+ curated datasets and 20+ model architectures.

RDKit is a comprehensive cheminformatics skill that guides users through molecular analysis tasks including reading/writing chemical structures (SMILES, SDF), calculating molecular descriptors (LogP, TPSA, molecular weight), generating fingerprints for similarity searching, and performing substructure matching. It includes ready-to-use Python scripts for drug-likeness screening, similarity searches, and functional group filtering.

Molfeat is a comprehensive guide for molecular featurization in machine learning. It provides documentation for converting chemical structures (SMILES strings) into numerical representations using 100+ featurizers including fingerprints (ECFP, MACCS), descriptors (RDKit, Mordred), and pretrained models (ChemBERTa, GIN). Ideal for QSAR modeling, virtual screening, and cheminformatics tasks.

This skill helps chemists and drug discovery researchers filter and prioritize compound libraries using established medicinal chemistry rules like Lipinski's Rule of Five, PAINS filters, and structural alerts. It can process molecules in batch with parallel processing and generate detailed filtering reports.