--> --- name: 'molecule-evolution-agent' description: 'Evolve Molecules' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Molecule Evolution Agent** acts as an autonomous medicinal chemist. It takes a starting molecule (or uses a default like Aspirin) and iteratively modifies its structure to optimize binding for a specific protein target.
Installs into .claude/skills of the current project.
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---
name: 'molecule-evolution-agent'
description: 'Evolve Molecules'
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
- read_file
- run_shell_command
---
# Molecule Evolution Agent
The **Molecule Evolution Agent** acts as an autonomous medicinal chemist. It takes a starting molecule (or uses a default like Aspirin) and iteratively modifies its structure to optimize binding for a specific protein target.
## When to Use This Skill
* **Lead Optimization**: When you have a hit molecule and want to improve its potency.
* **De Novo Design**: To explore chemical space around a target protein.
* **Idea Generation**: To get creative structural modifications suggested by an LLM.
## Core Capabilities
1. **SMILES Manipulation**: Reads and writes chemical structures in SMILES format.
2. **LLM Chemist**: Uses an LLM to suggest chemically valid modifications (e.g., "Add a fluorine group to the ring").
3. **Mock Scoring**: (Currently) Uses a mock scoring function to simulate docking affinity.
## Workflow
1. **Input**: Target Protein Name (e.g., "GPRC5D").
2. **Process**:
* Start with a seed molecule.
* Loop for *N* generations.
* Ask LLM for a modification.
* Score the new molecule.
* Keep the best candidate.
3. **Output**: Top candidate SMILES and the evolution history.
## Example Usage
**User**: "Design a better binder for GPRC5D."
**Agent Action**:
```bash
python3 Skills/Drug_Discovery/Molecule_Design/evolution_agent.py
# (Note: The script currently defaults to GPRC5D, but can be extended for arguments)
```
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
