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OpenClaw-Medical-Skills protein-structure-prediction

<!--

install
source · Clone the upstream repo
git clone https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/protein-structure-prediction" ~/.claude/skills/freedomintelligence-openclaw-medical-skills-protein-structure-prediction && rm -rf "$T"
OpenClaw · Install into ~/.openclaw/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills "$T" && mkdir -p ~/.openclaw/skills && cp -r "$T/skills/protein-structure-prediction" ~/.openclaw/skills/freedomintelligence-openclaw-medical-skills-protein-structure-prediction && rm -rf "$T"
manifest: skills/protein-structure-prediction/SKILL.md
tags
#protein-folding#structure-prediction#esmfold#alphafold3#pdb-generation
source content
<!-- # 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. # # Provenance: Authenticated by MD BABU MIA -->

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:

python3 Skills/Drug_Discovery/Protein_Structure/esmfold_client.py \
    --sequence "MKTIIALSYIFCLVFDYDY" \
    --output structure.pdb
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->