Drug Design Python Packages

prolif

Interaction Fingerprints for protein-ligand complexes and more

meeko

Interface for AutoDock, molecule parameterization

datamol

Molecular Processing Made Easy.

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.

molscore

A scoring, benchmarking and evaluation framework for goal directed generative models

moldrug

moldrug is a python package for drug-oriented optimization on the chemical space.

microberx

MicrobeRX

seqme

Metrics for evaluating biological sequence design

bindflow

A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS

molcraftdiffusion

A generative AI framework for 3D molecular generation and data-driven molecular design in computational chemistry.

scopy

An integrated negative design python library for desirable HTS/VS database design

cremdock

CReM-dock: molecule generation and decoration guided by molecular docking

matcha

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

toff

TOFF: (Topologies from Open Force Fields) is a Python package to get OpenFF, GAFF and Espaloma topologies for MD simulations.

tangelo-gc

A python package for exploring end-to-end chemistry workflows on quantum computers and simulators.

ensemble-md

A python package for performing GROMACS simulation ensembles

txgnn

TxGNN: Zero-shot prediction of therapeutic use with geometric deep learning and clinician centered design

lohi-splitter

Lo-Hi Splitter for Modern Splits of Molecular Datasets

transrot

Lightweight Python package to calculate translational vector and rotational matrix between two sets of 3D coordinates

bbb-calculator

Implements the blood brain barrier score described in: J. Med. Chem. 2019, 62, 21, 9824-9836 (https://doi.org/10.1021/acs.jmedchem.9b01220)

palmiche

A python package for automation of MD simulations