Predict protein structures locally and compare them to PDB references.
npx skills add https://github.com/ClawBio/ClawBio --skill struct-predictor
Please help me install this Agent Skill. Skill: struct-predictor Source: https://github.com/ClawBio/ClawBio/tree/main/skills/struct-predictor Command: npx skills add https://github.com/ClawBio/ClawBio --skill struct-predictor
Many researchers and clinicians need accurate, reproducible 3D protein models and comparisons to experimental structures without sending sensitive data to the cloud; this Skill enables local prediction, retrieval, and quantitative comparison of protein structures to support variant interpretation, model validation, and visualization.
Predict the 3D structure of the protein sequence MVLSPADKTNVKAA using ColabFold locally and compare the result to PDB ID 1A3N.
High-intent search queries and answers about installing and using this skill.
Predict protein structures locally by providing amino-acid sequences to predictors like ColabFold, Boltz, or Chai, then fetch experimental PDB structures to compute RMSD and TM-score for quantitative comparison.
Yes, you can compute RMSD and TM-score by fetching experimental PDB structures and comparing them against local AlphaFold predictions, enabling quantitative model validation and variant interpretation.
Yes, local installation of at least one predictor such as colabfold_batch, boltz, or chai is required, along with Python libraries like biopython and py3Dmol for PDB parsing and visualization.
Visualize pLDDT and PAE confidence maps by generating 3D renders and confidence plots from local prediction outputs, which can be compiled into reproducible markdown reports for interactive inspection or publication.
Yes, running local batch predictions using AlphaFold, Boltz, or Chai ensures sensitive amino-acid sequences remain on-premise, supporting reproducible variant interpretation and model validation without cloud data transfer.
Generate reproducible markdown reports by compiling 3D visualizations, pLDDT and PAE confidence plots, and RMSD comparison tables from local protein structure prediction and analysis outputs.
PKU-YuanGroupConverts PDF documents to clean, structured Markdown.
ANakaAnalyze AlphaFold/ESMFold predictions and visualize pLDDT and pAE confidence metrics in PyMOL.
jaechang-hitsRetrieve AlphaFold DB protein structures by UniProt ID and download PDB/mmCIF files.
MDheweiAlign two protein structures by Cα superimposition to compute global RMSD and per-residue deviations.
