mechanistic-ddi-pipeline

Mechanistic DDI Pipeline (cross-stack orchestrator)

Overview

This skill is the GLUE between two servers. It fuses ToolUniverse knowledge (CYP/UGT/transporter roles, DDI records, FDA labels, literature) with Schrodinger structure-level computation (3D generation, drug-likeness descriptors, QikProp ADMET, optional Glide docking) into one perpetrator-victim DDI verdict. It does not replace the deep tooluniverse-drug-drug-interaction skill - it adds the structure layer.

Stacks used:

• tooluniverse MCP (knowledge) - see the ddi-admet-research and tooluniverse-drug-drug-interaction skills for routing and tool details.
• schrodinger MCP (structure) - see the schrodinger-maestro-driver skill for the 12 tools, the license-token split, and the full prep -> grid -> dock -> MM-GBSA pipeline (glide_grid builds the grid in-server).

When to Use

• A DDI question where mechanism must be backed by both pathway knowledge AND molecular evidence (descriptors, ADMET, or a docking pose into a CYP/target structure).
• A novel or under-documented compound (limited DDI records) where structure-derived properties inform the prediction.
• A case where you must reconcile a knowledge-base claim with computed physchem/ADMET (e.g., does the structure support the proposed CYP-substrate role).

If the question is purely knowledge-based, use ddi-admet-research instead - do not spin up structure tools unnecessarily.

Orchestrated Workflow

1. Frame the pair with the perpetrator-victim model (who changes whom). Apply the CYP/UGT reasoning from tooluniverse-drug-drug-interaction BEFORE any tool call.

Conflict Resolution

Common Mistakes

Related Skills