google-deepmind/science-skills▌

### Alphafold Database Fetch And Analyze - name: "alphafold-database-fetch-and-analyze" - description: "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,..."

### Opentargets Database - name: "opentargets-database" - description: "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 - name: "pdb-database" - description: "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 simi..."

### Literature Search Openalex - name: "literature-search-openalex" - description: "Query the OpenAlex scholarly database for research papers, authors, institutions, topics, sources, publishers, funders, geo-locations, and keywords. Use when searching academic papers, resolving DOIs,..."

### Alphagenome Single Variant Analysis - name: "alphagenome-single-variant-analysis" - description: "Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about ..."

### Literature Search Arxiv - name: "literature-search-arxiv" - description: "Search for scientific papers, preprints, and publications on arXiv. Extract metadata, abstracts, and download full-text PDFs or HTML versions of papers. Use when the user asks to find research papers,..."

### Pymol - name: "pymol" - description: "Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure dis..."

### Clinical Trials Database - name: "clinical-trials-database" - description: "Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count..."

### Dbsnp Database - name: "dbsnp-database" - description: "Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings. For an rs..."

### Jaspar Database - name: "jaspar-database" - description: "Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene sym..."

### Literature Search Europepmc - name: "literature-search-europepmc" - description: "Search Europe PMC for scientific literature and download open-access full texts and PDFs. Retrieve full-text XML/plain text by PMCID, get citation lists and bibliography."

### Clinvar Database - name: "clinvar-database" - description: "Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic var..."

### Uniprot Database - name: "uniprot-database" - description: "Access protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef. Use when searching for proteins, mapping identifiers, or retrieving functional annotations and publica..."

### Unibind Database - name: "unibind-database" - description: "Queries the UniBind database for experimentally validated transcription factor (TF) binding sites. Use when retrieving direct TF-DNA interaction datasets, downloading binding site coordinates (BED/FAS..."

### Quickgo Database - name: "quickgo-database" - description: "Query the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find genes associated wit..."

### Workflow Skill Creator - name: "workflow-skill-creator" - description: "Distills a completed user workflow or interaction into a reusable agent skill. Use when the user asks to turn their workflow, interaction, or multi-step process into a skill, or when they say "make th..."

### Gnomad Database - name: "gnomad-database" - description: "Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-func..."

### Uv - name: "uv" - description: "Checks whether the uv Python package manager is installed and installs it if missing. Ensures uv is on PATH. Use when another skill requires uv as a prerequisite."

### Pubchem Database - name: "pubchem-database" - description: "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."

### Human Protein Atlas Database - name: "human-protein-atlas-database" - description: "Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA)."

### Ucsc Conservation And Tfbs - name: "ucsc-conservation-and-tfbs" - description: "Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser. Use when analyzing whether genomic variants or regions are evolut..."

### String Database - name: "string-database" - description: "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, confi..."

### Pubmed Database - name: "pubmed-database" - description: "Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to dis..."

### Gtex Database - name: "gtex-database" - description: "Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites."

### Ensembl Database - name: "ensembl-database" - description: "Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP)...."

### Scienceskillscommon - name: "scienceskillscommon" - description: "Shared Python package for Science Skills, currently containing http_client -- a unified HTTP client with rate limiting, retries, and exponential backoff. Not a standalone agent skill. Do not invoke di..."

### Protein Sequence Similarity Search - name: "protein-sequence-similarity-search" - description: "Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find ho..."

### Literature Search Biorxiv - name: "literature-search-biorxiv" - description: "Browse, filter, and download life sciences, biology, and medical preprints from bioRxiv and medRxiv. Supports fetching paper metadata by DOI, and browsing by date range with category and keyword filte..."

### Reactome Database - name: "reactome-database" - description: "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..."

### Embl Ebi Ols - name: "embl-ebi-ols" - description: "Query and search the EMBL-EBI Ontology Lookup Service (OLS) for biomedical ontology terms, definitions, and hierarchies across 250+ ontologies (e.g., GO, DOID, HP). Use when the user asks to search fo..."

### Chembl Database - name: "chembl-database" - description: "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 mechan..."

### Interpro Database - name: "interpro-database" - description: "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. In..."

### Encode Ccres Database - name: "encode-ccres-database" - description: "Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.). Use when..."

### Protein Sequence Msa - name: "protein-sequence-msa" - description: "Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports ..."

### Foldseek Structural Search - name: "foldseek-structural-search" - description: "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, ..."

### Openfda Database - name: "openfda-database" - description: "Query, search, and download data from the openFDA API for drugs, devices, foods, tobacco, cosmetics, animal and veterinary products, substances, and transparency data. Use for FDA adverse events, reca..."

### Ncbi Sequence Fetch - name: "ncbi-sequence-fetch" - description: "Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent ..."