aaindex Documentation
aaindex is a lightweight Python package for accessing the data in the AAindex databases, which represent the physicochemical, biochemical, and structural properties of amino acids as numerical indices. The AAindex database, maintained by the Kyoto Encyclopedia of Genes and Genomes (KEGG), is a widely-used reference resource in bioinformatics and computational biology, providing curated amino acid property data derived from published literature.
This package offers a simple, dependency-free interface for querying any record across all three AAindex databases. Records can be retrieved by their accession number or searched by keyword, and individual fields — including numerical values, descriptions, references, and correlation coefficients — are all directly accessible. It is well-suited for use in protein sequence analysis, feature engineering for machine learning models, and any application that requires standardised amino acid physicochemical data.
The package is used other key custom-built projects: pySAR and protpy.
The package supports all three AAindex databases:
AAindex1 — 566 amino acid indices (single numerical values per amino acid)
AAindex2 — 94 amino acid substitution matrices (20 x 20)
AAindex3 — 47 amino acid contact potential matrices (20 x 20)
User Guide
Database Reference
Project