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: Evolve Molecules4---56<!--7# COPYRIGHT NOTICE8# This file is part of the "Universal Biomedical Skills" project.9# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>10# All Rights Reserved.11#12# This code is proprietary and confidential.13# Unauthorized copying of this file, via any medium is strictly prohibited.14#15# Provenance: Authenticated by MD BABU MIA1617-->18192021# Molecule Evolution Agent2223The **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.2425## When to Use This Skill2627* **Lead Optimization**: When you have a hit molecule and want to improve its potency.28* **De Novo Design**: To explore chemical space around a target protein.29* **Idea Generation**: To get creative structural modifications suggested by an LLM.3031## Core Capabilities32331. **SMILES Manipulation**: Reads and writes chemical structures in SMILES format.342. **LLM Chemist**: Uses an LLM to suggest chemically valid modifications (e.g., "Add a fluorine group to the ring").353. **Mock Scoring**: (Currently) Uses a mock scoring function to simulate docking affinity.3637## Workflow38391. **Input**: Target Protein Name (e.g., "GPRC5D").402. **Process**: 41 * Start with a seed molecule.42 * Loop for *N* generations.43 * Ask LLM for a modification.44 * Score the new molecule.45 * Keep the best candidate.463. **Output**: Top candidate SMILES and the evolution history.4748## Example Usage4950**User**: "Design a better binder for GPRC5D."5152**Agent Action**:53```bash54python3 Skills/Drug_Discovery/Molecule_Design/evolution_agent.py55# (Note: The script currently defaults to GPRC5D, but can be extended for arguments)56```575859<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add fridrichmethod/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.
Evolve Molecules It is listed under AI & ML on SkillMD.
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FridrichMethod (@fridrichmethod) published this skill. Their other Agent Skills are listed on their SkillMD profile.
FridrichMethod