Chemcrow Drug Discovery

---
name: 'chemcrow-drug-discovery'
description: 'An LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design.'
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
  - read_file
  - run_shell_command
---

<!--
# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
#
# Provenance: Authenticated by MD BABU MIA

-->



# ChemCrow

ChemCrow is an open-source package for the accurate integration of Large Language Models (LLMs) with chemistry tools. It is designed to autonomously plan and execute chemical syntheses, research materials, and discover new drugs.

## When to Use This Skill

*   **Synthesis Planning**: "How do I synthesize Ibuprofen?"
*   **Property Prediction**: "What is the logP of this molecule?"
*   **Safety Checks**: "Is this reaction explosive?"
*   **Literature Search**: "Find patents related to this substructure."

## Core Capabilities

1.  **Synthesis Planning**: Uses tools like RXN4Chemistry or local retrosynthesis models to plan routes.
2.  **Molecule Manipulation**: Add/remove functional groups, generate SMILES (RDKit).
3.  **Safety Assessment**: Checks reagents against safety databases (PubChem, GHS).
4.  **Web Search**: Google/Patent search for chemical literature.

## Tools (Expanded List - v2.0)

*   **RDKit**: Cheminformatics (MolToSmiles, SmilesToMol, descriptors).
*   **PubChem**: Search for properties and safety data.
*   **LiteratureSearch**: Search arXiv, patents.
*   **Synthesis**: IBM RXN, OPLS.
*   **Name2SMILES**: Convert chemical names to structures.

## Example Usage

**User**: "Plan a synthesis for a derivative of Aspirin that might have better solubility."

**Agent Action**:
1.  Retrieves Aspirin structure (SMILES).
2.  Modifies structure (e.g., adds a polar group) using RDKit.
3.  Checks solubility prediction.
4.  Plans synthesis route for the new molecule.
5.  Checks safety of reagents.

<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->