Drug Discovery Python Packages

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

nequip

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

nequip-allegro

Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials

prolif

Interaction Fingerprints for protein-ligand complexes and more

deepchem

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

drug-named-entity-recognition

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

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

meeko

Interface for AutoDock, molecule parameterization

datamol

Molecular Processing Made Easy.

chemprop

Message Passing Neural Networks for Molecule Property Prediction

biopandas

Working with molecular structures in pandas DataFrames

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

dgllife

Python package for graph neural networks in chemistry and biology

hbat

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

bingo-elastic

Universal cheminformatics toolkit, utilities and database search tools

bblean

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

graphein

Protein Graph Library

fragmenstein

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

deeppurpose

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

uniprot-mcp-server

Model Context Protocol server for UniProt — Swiss-Prot and TrEMBL protein knowledgebase. 41 tools across 8 families with per-query SHA-256 provenance verification and offline replay.

acellera-htmd

HTMD: Programming Environment for Molecular Discovery

proteinfp

End-to-end protein function prediction from structure alone: active sites, binding pockets, GO terms, PPI partners, and drug candidates.

alethiotx

Alethio Therapeutics Python Toolkit

ersilia

A hub of AI/ML models for open source drug discovery and global health