Drug Discovery Python Packages

pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

chematic

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

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

renkin

Local and reproducible route auditing for AiZynthFinder, Syntheseus and RENKIN — plus a portable Rust retrosynthesis engine.

datamol

Molecular Processing Made Easy.

chemprop

Message Passing Neural Networks for Molecule Property Prediction

meeko

Interface for AutoDock, molecule parameterization

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)

biopandas

Working with molecular structures in pandas DataFrames

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 https://hbat-web.abhishek-tiwari.com

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

nequip

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

pertpy

Single-cell perturbation analysis

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)

bblean

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

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

graphein

Protein Graph Library

alphafold-sovereign-mcp

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

opentargets-mira

Multi-source Indication & Report Analytics

fragmenstein

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