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

seqme

Metrics for evaluating biological sequence design

microberx

MicrobeRX

moldrug

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

scopy

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

matcha

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

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

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.

toff

toff is a python package to get topologies from open force fields.

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

Train-test splitter for Lead Optimization and Hit Identification tasks.

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

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)