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.
1---2name: protein-structure-prediction3description: <!--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: 'protein-structure-prediction'20description: 'Predicts 3D protein structures from amino acid sequences using ESMFold or AlphaFold3 (mock).'21measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.22allowed-tools:23 - read_file24 - run_shell_command25---262728# Protein Structure Prediction (ESMFold/AF3)2930The **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).3132## When to Use This Skill3334* When you have a protein sequence and need its 3D coordinates.35* To check if a designed sequence folds into a stable structure.36* To prepare a receptor for docking simulations.3738## Core Capabilities39401. **Folding**: Generates atomic coordinates (PDB format).412. **Confidence Scoring**: Returns pLDDT scores per residue.423. **Visualization**: (Optional) Generates a static view of the structure.4344## Workflow45461. **Input**: Amino acid sequence (FASTA string).472. **Process**: Sends sequence to ESMFold API (or local inference).483. **Output**: Saves `.pdb` file and returns confidence metrics.4950## Example Usage5152**User**: "Fold this sequence: MKTIIALSY..."5354**Agent Action**:55```bash56python3 Skills/Drug_Discovery/Protein_Structure/esmfold_client.py \57 --sequence "MKTIIALSYIFCLVFDYDY" \58 --output structure.pdb59```60616263<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add biotender-max/protein-structure-prediction 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.
<!-- It is listed under Coding & Dev Tools on SkillMD.
This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.
This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.
Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.
BioTender-max (@biotender-max) published this skill. Their other Agent Skills are listed on their SkillMD profile.
BioTender-max