AlphaFold DB MCP has basic tool definitions with schemas and descriptions, but significant gaps limit production readiness. All 4 tools have input schemas with type definitions and descriptions present. However, naming lacks action verbs (prediction, summary, annotations, uniprot are nouns/identifiers, not verb_noun patterns like get_prediction). Parameter descriptions are minimal (10-30 chars, well below the 72-char baseline). Output schemas are completely undocumented, LLMs cannot plan downstream calls or extract structured data. Error handling is generic (404 → 'not found', non-200 → status code + truncated text). No parameter validation guidance, no enum constraints, no pagination support despite API returning potentially large result sets. The 'qualifier' parameter appears in 3 tools but lacks format guidance (is it case-sensitive? What's the valid format?). Tools 'prediction' and 'uniprot' appear to be duplicates with different parameter names, violating single-responsibility and composition patterns.

• Rename tools with action verbs: 'get_alphafold_prediction', 'get_protein_summary', 'list_sequence_annotations', 'fetch_uniprot_structure'. This matches verb_noun baseline and clarifies intent.
• Document output schemas for each tool. Example for 'prediction': 'Returns {pdb_url: string, cif_url: string, pae_url: string, plddt_score: number, organism: string, sequence_length: number}'. Include all fields LLMs need for downstream calls.
• Expand parameter descriptions. For 'qualifier'/'uniprot_id': 'UniProt accession (e.g. P00533). Case-sensitive, 6-10 alphanumeric characters. Required.' Add format constraints and examples.
• Consolidate 'prediction' and 'uniprot' into a single tool with a single parameter name (e.g. 'uniprot_accession'). Reduces cognitive load and eliminates duplication.
• Improve error messages with recovery guidance. E.g. '404: Accession "P00533" not found. Verify the UniProt accession is correct (format: 6-10 alphanumeric chars). Try searching UniProt directly if unsure.'