Best use case
protein-structure-prediction is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
COPYRIGHT NOTICE
Teams using protein-structure-prediction should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/protein-structure-prediction/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How protein-structure-prediction Compares
| Feature / Agent | protein-structure-prediction | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
COPYRIGHT NOTICE
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
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# 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.
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---
name: 'protein-structure-prediction'
description: 'Predicts 3D protein structures from amino acid sequences using ESMFold or AlphaFold3 (mock).'
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
- read_file
- run_shell_command
---
# Protein Structure Prediction (ESMFold/AF3)
The **Protein Structure Prediction Skill** provides an interface to state-of-the-art folding models. It takes an amino acid sequence and returns a PDB file or structure metrics (pLDDT).
## When to Use This Skill
* When you have a protein sequence and need its 3D coordinates.
* To check if a designed sequence folds into a stable structure.
* To prepare a receptor for docking simulations.
## Core Capabilities
1. **Folding**: Generates atomic coordinates (PDB format).
2. **Confidence Scoring**: Returns pLDDT scores per residue.
3. **Visualization**: (Optional) Generates a static view of the structure.
## Workflow
1. **Input**: Amino acid sequence (FASTA string).
2. **Process**: Sends sequence to ESMFold API (or local inference).
3. **Output**: Saves `.pdb` file and returns confidence metrics.
## Example Usage
**User**: "Fold this sequence: MKTIIALSY..."
**Agent Action**:
```bash
python3 Skills/Drug_Discovery/Protein_Structure/esmfold_client.py \
--sequence "MKTIIALSYIFCLVFDYDY" \
--output structure.pdb
```
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