Molecular Docking Python Packages

spindry

Low-cost host-guest conformer generation

ocdocker

OCdocker is a docking automation suite with scoring functions consensus based on ML

easydock

Fully automated docking pipeline (can be run in distributed environments)

pyscreener

pythonic interface to virtual screening software

novomcp

The open computational chemistry engine for drug discovery and materials science; MCP + REST + Workbench + Next.js dashboard, wrapping RDKit, GROMACS, AutoDock, OpenFold, Chai, Boltz, Gnina.

cellsim

Physics-first, uncertainty-honest in-silico cell and drug-response simulator (Python). Validated docking/ADMET input layer (Vina, OpenFF, xTB), cell-level PK/PD modules, and a cell/colony engine under construction toward a validated interactive dish.

ladock

LADOCK — molecular docking workstation in one package, two front-ends: ladock-cli (rule-based agent) and ladock-desktop (PySide6 GUI)

lazydock

LazyDock: Lazy Dock, Easy Life

karyon

Legible, deterministic QC/qualification for bio-AI tool outputs — named-reason contracts + agent skills that compose with NVIDIA BioNeMo.

polypharm

A Python-based library to perform IFD and MM/GBSA calculations on different targets using a polypharmacological approach.

dok2any

Dok2any is a small Python package designed to convert dok files generated by LeDock molecular docking software, a non-standard chemical structure file format unique for LeDock, to various other chemical structure formats using Openbabel.

matcha

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

docktdeep

CNN-based protein-ligand scoring function.

docktgrid

Generate customized voxel representations of protein-ligand complexes using GPU.

posebench

Comprehensive benchmarking of protein-ligand structure prediction methods. (Nature Machine Intelligence)

moldock

Fully automated docking pipeline (can be run in distributed environments)

pyplif-hippos

HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS