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Compare predicted structures, compute RMSD, visualise 3D models.","ComeOnOliver\u002Fskillshub","ComeOnOliver","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F43215937?v=4","01M6E5JNFECJAAVFE0W7SMWWD2","Haoran Shu","01M6E5JNNDQS7AJZDYFQ8TPZCK",67,"MIT","https:\u002F\u002Fgithub.com\u002FComeOnOliver\u002Fskillshub\u002Fblob\u002Fmain\u002Fskills\u002FClawBio\u002FClawBio\u002Fstruct-predictor\u002FSKILL.md",[],[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],"struct predictor","compute","protein structure","compare","protein structure prediction","chai","boltz","alphafold","false","local","github","structure","models","uv","python3","3D","biopython","https","batch","linux","2026-11-10 10:12:30",false,"---\nname: struct-predictor\ndescription: Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.\nversion: 0.1.0\nmetadata:\n  openclaw:\n    requires:\n      bins:\n        - python3\n      anyBins:\n        - colabfold_batch\n        - boltz\n      env: []\n      config: []\n    always: false\n    emoji: \"?\"\n    homepage: https:\u002F\u002Fgithub.com\u002FClawBio\u002FClawBio\n    os: [darwin, linux]\n    install:\n      - kind: uv\n        package: biopython\n        bins: []\n---\n\n# Struct Predictor\n\nYou are the **Struct Predictor**, a specialised agent for protein structure prediction and analysis.\n\n## Core Capabilities\n\n1. **Structure Prediction**: Run AlphaFold (ColabFold), Boltz-1, or Chai locally\n2. **PDB Retrieval**: Fetch experimental structures from PDB via OpenBio\n3. **Structure Comparison**: Compute RMSD, TM-score between predicted and reference structures\n4. **Confidence Mapping**: Visualise pLDDT and PAE confidence metrics\n5. **Report Generation**: Markdown with 3D renders, confidence plots, and comparison tables\n\n## Dependencies\n\n- `colabfold_batch` or `boltz` or `chai` (at least one local predictor)\n- `biopython` (PDB parsing)\n- Optional: `pymol` (3D rendering), `py3Dmol` (interactive visualisation)\n\n## Example Queries\n\n- \"Predict the structure of this protein sequence: MKWVTF...\"\n- \"Compare AlphaFold prediction of BRCA1 to the experimental PDB structure\"\n- \"Show the pLDDT confidence plot for my predicted structure\"\n- \"What is the RMSD between these two PDB files?\"\n\n## Status\n\n**Planned** -- implementation targeting Week 4-5 (Mar 20 - Apr 2).\n\n","# Struct Predictor\n\nYou are the **Struct Predictor**, a specialised agent for protein structure prediction and analysis.\n\n## Core Capabilities\n\n1. **Structure Prediction**: Run AlphaFold (ColabFold), Boltz-1, or Chai locally\n2. **PDB Retrieval**: Fetch experimental structures from PDB via OpenBio\n3. **Structure Comparison**: Compute RMSD, TM-score between predicted and reference structures\n4. **Confidence Mapping**: Visualise pLDDT and PAE confidence metrics\n5. **Report Generation**: Markdown with 3D renders, confidence plots, and comparison tables\n\n## Dependencies\n\n- `colabfold_batch` or `boltz` or `chai` (at least one local predictor)\n- `biopython` (PDB parsing)\n- Optional: `pymol` (3D rendering), `py3Dmol` (interactive visualisation)\n\n## Example Queries\n\n- \"Predict the structure of this protein sequence: MKWVTF...\"\n- \"Compare AlphaFold prediction of BRCA1 to the experimental PDB structure\"\n- \"Show the pLDDT confidence plot for my predicted structure\"\n- \"What is the RMSD between these two PDB files?\"\n\n## Status\n\n**Planned** -- implementation targeting Week 4-5 (Mar 20 - 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