mdhewei/bioinfor-claw/protein-structure-for-gene

Protein Structure Analysis for Gene

Purpose

For a given gene symbol, retrieve comprehensive protein structural information:

• UniProt canonical accession + protein metadata
• Domain and functional feature annotations (UniProt)
• Experimental PDB structures (RCSB) with method and resolution
• AlphaFold2 predicted structure entry (EBI)
• Publication-quality linear domain map figure

Supported modules:

• uniprot — protein metadata + domain/feature annotations
• pdb — experimental PDB structures from RCSB
• alphafold — AlphaFold2 predicted structure entry
• domain_map — linear domain figure (requires uniprot)
• all — run all modules (default)

Reuse policy

This skill is designed for:

• Structural context for any gene of interest
• Validating domain boundaries before designing experiments
• AlphaFold availability check for a protein
• Downstream workflows that need PDB IDs or UniProt accessions
• Summarising experimental vs predicted structural coverage

This skill does not require local data files. All data is fetched live from public APIs.

Data sources

Inputs

Required

• --gene — gene symbol (e.g. EGFR, TP53, BRCA1, KRAS)
• --outdir — output directory

Optional

• --organism

Default: human Also supports: mouse, rat, or any NCBI taxon ID

• --modules

Default: all Comma-separated list: uniprot, pdb, alphafold, domain_map Example: --modules uniprot,domain_map

• --max-pdb

Default: 20 Maximum number of PDB structures to retrieve.

Outputs

Always

• protein_structure_summary.tsv — one-row summary of all results
• summary.txt — human-readable version of the summary

UniProt module

• <GENE>.<ACCESSION>.features.tsv

All annotated features with columns: type, description, start, end, length

Feature types include: Domain, Region, Motif, Binding site, Active site, Signal, Transmembrane, Coiled coil, Compositional bias, and more.

PDB module

• <GENE>.<ACCESSION>.pdb_structures.tsv

Columns: pdb_id, title, method, resolution_A, n_protein_chains, n_atoms, pubmed_id, authors, deposition_date, rcsb_url

AlphaFold module

• <GENE>.<ACCESSION>.alphafold.tsv

Columns: alphafold_id, uniprot_accession, gene, organism, seq_length, model_created, latest_version, pdb_url, cif_url, pae_image_url, alphafold_page

Domain map module

• <GENE>.<ACCESSION>.domain_map.png (300 dpi)
• <GENE>.<ACCESSION>.domain_map.pdf

Linear schematic with colour-coded feature types, row-stacked to prevent overlaps, log-rank annotation style consistent with other skills.

Parameter decision guide

Execution policy

Construct the command from gene, organism, and module selection.

Command template

python scripts/protein_structure_for_gene.py \
  --gene <GENE> \
  [--organism <ORGANISM>] \
  [--modules <MODULES>] \
  [--max-pdb <N>] \
  --outdir <OUTDIR>

Example commands

Full analysis (default)

python scripts/protein_structure_for_gene.py \
  --gene EGFR \
  --outdir results/

UniProt domains + domain map only

python scripts/protein_structure_for_gene.py \
  --gene TP53 \
  --modules uniprot,domain_map \
  --outdir results/

PDB structures only (up to 50)

python scripts/protein_structure_for_gene.py \
  --gene BRCA1 \
  --modules pdb \
  --max-pdb 50 \
  --outdir results/

AlphaFold check for mouse gene

python scripts/protein_structure_for_gene.py \
  --gene Trp53 \
  --organism mouse \
  --modules alphafold \
  --outdir results/

All modules for a kinase

python scripts/protein_structure_for_gene.py \
  --gene BRAF \
  --modules all \
  --outdir results/

Domain map behaviour

• Feature types drawn: Domain, Region, Motif, Binding site, Active site,

Signal, Transmembrane, Coiled coil

• Each feature type is assigned a distinct colour (shown in legend)
• Features are row-stacked to prevent overlap
• Feature labels are shown inside boxes when wide enough (> 4% of sequence length)
• Both PNG (300 dpi) and PDF are saved

Failure conditions

Fail clearly if:

• --gene is missing or cannot be resolved in UniProt for the given organism
• --outdir is missing or cannot be written to
• --modules contains an unrecognised module name
• UniProt API returns no results (try alternate gene name or organism)
• domain_map is requested but no features are found in UniProt

Agent trigger examples

Trigger this skill when the user asks:

• "What domains does EGFR have?"
• "Show me the protein structure information for TP53"
• "Is there an AlphaFold structure for KRAS?"
• "How many PDB structures exist for BRCA1?"
• "Draw a domain map for MYC"
• "What's the best resolution crystal structure of CDK2?"
• "Get UniProt annotation and PDB entries for PTEN"
• "What functional regions are annotated in PIK3CA?"

Do NOT trigger this skill when the user asks:

• "Predict a protein structure from sequence" → requires local folding tool (e.g. AlphaFold2 CLI)
• "Compare two protein structures" → structural alignment, out of scope
• "Show me TCGA expression for EGFR" → use tcga-expression-for-gene
• "Perform docking analysis" → requires specialised docking software

Notes

• An internet connection is required; all data is fetched live.
• UniProt resolution prefers reviewed (Swiss-Prot) entries.

For unreviewed proteins, results may be less complete.

• PDB search is based on UniProt cross-references in RCSB.

Structures deposited without UniProt mapping will not appear.

• AlphaFold coverage is nearly complete for human proteins

and expanding for other organisms. A 404 means no entry exists yet.

• For multi-domain proteins, the domain map may have multiple stacked rows.

This is expected behaviour, not an error.

• Mouse gene symbols often use title-case (e.g. Trp53, not TP53).

Specify --organism mouse for correct UniProt resolution.