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molclaw-esmfold

Predict 3D protein structures from amino acid sequences using ESMFold.

28|2|Updated Mar 31, 2026
Search Tags:#bioinformatics#pdb#plddt#protein-structure#structure-prediction#esmfold#sequence-prediction
One-click install
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-esmfold
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molclaw-esmfold
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-esmfold
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-esmfold

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill converts an amino-acid sequence into a predicted 3D protein structure (PDB) using the ESMFold model, removing manual setup and ensuring model confidence metrics are available for verification.

Core Features & Use Cases

  • ESMFold prediction: generate predicted PDB files from single protein sequences.
  • Confidence assessment: pLDDT scores are recorded in the B-factor column and guidance is provided for interpreting confidence thresholds.
  • Reproducibility and download policy: requires downloading all structure outputs to the local workspace for verification and downstream analysis.
  • Use Case: run an ESMFold prediction for a protein under 800 residues, check pLDDT, map residue numbering if needed, and retrieve the PDB for docking or visualization.

Quick Start

Predict the 3D structure for the provided amino-acid sequence and download the resulting PDB file to the local workspace for verification.

Frequently Asked Questions about molclaw-esmfold

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I predict a protein 3D structure from an amino acid sequence?▼

You can predict a protein 3D structure from an amino acid sequence using ESMFold, which generates a downloadable PDB file with pLDDT confidence scores in the B-factor column for sequences typically under 800 residues.

How do I check pLDDT confidence scores for a predicted protein structure?▼

pLDDT confidence scores for a predicted protein structure are recorded in the B-factor column of the generated PDB file, allowing you to evaluate prediction reliability and interpret confidence thresholds during verification.

Can I use ESMFold for protein sequences over 800 residues?▼

ESMFold prediction through this tool is intended for protein sequences typically under 800 residues, so sequences exceeding this length may not be suitable for processing within this specific workflow.

How do I get a downloadable PDB file from a sequence prediction?▼

To get a downloadable PDB file from a sequence prediction, the tool enforces local download of all structure outputs to your workspace, ensuring the file is available for verification and downstream docking or visualization.

What is ESMFold single-sequence prediction used for?▼

ESMFold single-sequence prediction is used for converting amino acid sequences into predicted 3D protein structures without manual setup, providing confidence-aware evaluation and downloadable PDB outputs for workflows like docking.

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