Individual skill
protein-diagram
Publication-quality protein analysis diagrams. Domain architecture maps, secondary structure annotation, Ramachandran plots, contact maps, multiple sequence alignment visualization, and protein feature tracks.
backend/cli/skills/visualization/protein-diagram/SKILL.md
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# Protein Diagram
Generate publication-quality protein analysis diagrams for structural biology, bioinformatics, and drug discovery workflows. This skill provides tools for rendering domain architecture maps, secondary structure annotations, Ramachandran plots, residue contact maps, colored MSA visualizations, and protein feature tracks.
## When to Use
- **Domain architecture**: Pfam/InterPro-style domain maps showing functional domains, motifs, and regions along a protein sequence.
- **Secondary structure**: Helix/sheet/coil annotation tracks from PDB structures or DSSP assignments.
- **Ramachandran plots**: Phi/psi dihedral angle scatter plots for structure validation and quality assessment.
- **Contact maps**: Residue-residue distance or contact heatmaps from PDB structures for fold analysis.
- **MSA visualization**: Colored multiple sequence alignment plots showing conservation, gaps, and consensus.
- **Feature tracks**: Annotated protein feature maps showing PTMs, binding sites, mutations, and domain boundaries.
