alphafold-database-fetch-and-analyze

What problem does it solve?

This Skill solves the problem of quickly retrieving AlphaFold predicted structures for a specific protein and interpreting structural confidence and domain organization without manual, error-prone analysis.

Core Features & Use Cases

• UniProt-ID driven retrieval: Downloads AlphaFold Database mmCIF structures and Predicted Aligned Error (PAE) matrices using a required UniProt accession, with guardrails to prevent misuse when only a name/sequence is provided.
• pLDDT confidence analysis: Computes and reports global pLDDT plus fractions of very low, low, confident, and very high residues to assess overall ordering vs disorder.
• PAE-based rigid domain boundaries: Detects and summarizes rigid global domains (including residue ranges) by applying a sliding-window PAE heuristic and merging sub-domains.
• Operational edge-case warnings: Prominently relays canonical-vs-isoform substitutions and large-protein (>2700 aa) fragment warnings, and issues disorder-related warnings to discourage inappropriate downstream structural workflows.

Quick Start

Retrieve and analyze AlphaFold predictions for UniProt ID P00520 by instructing your agent: “Use alphafold-database-fetch-and-analyze to download the AlphaFold structure for UniProt P00520 and summarize pLDDT confidence and PAE domain boundaries.”