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
SMILES Manipulation: Reads and writes chemical structures in SMILES format.
LLM Chemist: Uses an LLM to suggest chemically valid modifications (e.g., "Add a fluorine group to the ring").
Mock Scoring: (Currently) Uses a mock scoring function to simulate docking affinity.
Workflow
Input: Target Protein Name (e.g., "GPRC5D").
Process:
Start with a seed molecule.
Loop for N generations.
Ask LLM for a modification.
Score the new molecule.
Keep the best candidate.
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)
1---2name: molecule-evolution-agent3description: <!--4---5<!--6# COPYRIGHT NOTICE7# This file is part of the "Universal Biomedical Skills" project.8# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>9# All Rights Reserved.10#11# This code is proprietary and confidential.12# Unauthorized copying of this file, via any medium is strictly prohibited.13#14# Provenance: Authenticated by MD BABU MIA1516-->1718---19name: 'molecule-evolution-agent'20description: 'Evolve Molecules'21measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.22allowed-tools:23 - read_file24 - run_shell_command25---262728# Molecule Evolution Agent2930The **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.3132## When to Use This Skill3334* **Lead Optimization**: When you have a hit molecule and want to improve its potency.35* **De Novo Design**: To explore chemical space around a target protein.36* **Idea Generation**: To get creative structural modifications suggested by an LLM.3738## Core Capabilities39401. **SMILES Manipulation**: Reads and writes chemical structures in SMILES format.412. **LLM Chemist**: Uses an LLM to suggest chemically valid modifications (e.g., "Add a fluorine group to the ring").423. **Mock Scoring**: (Currently) Uses a mock scoring function to simulate docking affinity.4344## Workflow45461. **Input**: Target Protein Name (e.g., "GPRC5D").472. **Process**: 48 * Start with a seed molecule.49 * Loop for *N* generations.50 * Ask LLM for a modification.51 * Score the new molecule.52 * Keep the best candidate.533. **Output**: Top candidate SMILES and the evolution history.5455## Example Usage5657**User**: "Design a better binder for GPRC5D."5859**Agent Action**:60```bash61python3 Skills/Drug_Discovery/Molecule_Design/evolution_agent.py62# (Note: The script currently defaults to GPRC5D, but can be extended for arguments)63```646566<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add biotender-max/molecule-evolution-agent in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.
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BioTender-max (@biotender-max) published this skill. Their other Agent Skills are listed on their SkillMD profile.
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