BeyondTheProtocol

alphafold-database-fetch-and-analyze

Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.

chembl-database

Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.

credentials

Instructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.

foldseek-structural-search

Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.

human-protein-atlas-database

Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).

interpro-database

Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N significantly expands annotation and sequence coverage with deep learning. Includes domain architecture (IDA) search.

opentargets-database

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

pdb-database

Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.

pubchem-database

Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.

reactome-database

Query the Reactome database (Analysis and Content Services). Use when the user asks about pathway analysis, gene list enrichment, retrieving results by token, finding unmapped or not-found identifiers, mapping identifiers, reaction participants (inputs, outputs), pathway hierarchy (including top-level pathways), diagram export, cross-reference mapping, or searching the knowledgebase.

string-database

Query the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology. Use when the user asks about interactions between specific proteins, interaction evidence, confidence scores, protein interaction partners, or pathway enrichments.

uniprot-database

Access protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef. Use when searching for proteins, mapping identifiers, or retrieving functional annotations and publications. Don't use for sequence alignment, protein folding, or sequence similarity search (use specialized skills for those tasks).

a11y

Estándares de accesibilidad web (WCAG 2.2 AA, WAI-ARIA APG) con más de 38 anti-patrones clasificados por severidad, contexto legal (EAA, ADA Title II) y arreglos concretos por framework. Úsala al construir o revisar cualquier superficie visible —web, dashboards, paneles, PDFs con HTML— y siempre que se toque color, foco, movimiento, semántica, formularios o áreas táctiles. La auditoría la firma el comité `diseno`; esto es la vara contra la que audita.