Drug Discovery Python Packages

chemprop

Message Passing Neural Networks for Molecule Property Prediction

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

drug-named-entity-recognition

Drug Named Entity Recognition library to find and resolve drug names in a string (drug named entity linking)

datamol

Molecular Processing Made Easy.

meeko

Interface for AutoDock, molecule parameterization

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

prolif

Interaction Fingerprints for protein-ligand complexes and more

nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

biopandas

Working with molecular structures in pandas DataFrames

dgllife

Python package for graph neural networks in chemistry and biology

chematic

A pure-Rust cheminformatics library targeting RDKit feature parity — zero C/C++ by default.

nequip-allegro

Allegro is a code for building highly scalable E(3)-equivariant interatomic potentials

renkin

RENKIN is an open-source retrosynthesis engine for computer-aided synthesis planning (CASP) that automatically discovers optimal chemical reaction routes from a target molecule back to cheap, commercially available starting materials.

alphafold-sovereign-mcp

Local-first biomedical MCP over AlphaFold DB + 8 public sources, with SQLite knowledge graph, offline mode, and explicit clinical-use limits.

uniprot-mcp-server

Auditable UniProt MCP server with per-response SHA-256 provenance, release pinning, verification, and offline replay.

bblean

BitBIRCH-Lean, a memory-efficient implementation of BitBIRCH designed for high-throughput clustering of huge molecular libraries

graphein

Protein Graph Library

bingo-elastic

Universal cheminformatics toolkit, utilities and database search tools

deeppurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

fragmenstein

Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse

acellera-htmd

HTMD: Programming Environment for Molecular Discovery