Drug Design Python Packages

datamol

Molecular Processing Made Easy.

meeko

Interface for AutoDock, molecule parameterization

prolif

Interaction Fingerprints for protein-ligand complexes and more

uniprot-mcp-server

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

molscore

An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular design

moldrug

moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ​

seqme

Metrics for evaluating biological sequence design

scopy

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

microberx

MicrobeRX

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.

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.

ensemble-md

A python package for performing GROMACS simulation ensembles

matcha

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

cremdock

CReM-dock: generation of chemically reasonable molecules guided by molecular docking

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

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)

transrot

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

palmiche

Group of scripts to automate pipelines during my PhD in Computational Biophysics