molecule-evolution-agent

<!--

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

-->

---

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.

1. Output: Top candidate SMILES and the evolution history.

Example Usage

User: "Design a better binder for GPRC5D."

Agent Action:

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 -->