cmxflow

b-shields/cmxflow

This connects Claude to cheminformatics workflows for drug discovery and molecular modeling. It exposes five tools: build_workflow lets you compose pipelines from 15+ blocks for ligand prep, clustering, docking, and virtual screening. run_workflow executes them, optimize_workflow tunes parameters end-to-end with Bayesian optimization via Optuna, manage_workflows handles serialization, and view_structures renders 3D molecules through PyMOL. Reach for this when you need to prepare molecules for docking, run similarity screens, enumerate stereoisomers, or optimize fingerprint parameters against benchmark datasets. The agent can chain blocks conversationally, like standardizing a library then filtering by Lipinski rules, without writing Python.

GitHub stars

2

tools

5

transport

STDIO

last updated

Jun 15, 2026

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