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Found 17 Skills
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.
Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For Chai prediction, use chai.
Design and evaluate vaccine candidates using computational immunology tools. Covers epitope prediction (MHC-I/II binding via IEDB), population coverage analysis, antigen selection, adjuvant matching, and immunogenicity assessment. Integrates IEDB for epitope prediction, UniProt for antigen sequences, PDB/AlphaFold for structural epitopes, BVBRC for pathogen proteomes, and literature for clinical precedent. Use when asked about vaccine design, epitope prediction, immunogenicity, MHC binding, T-cell epitopes, B-cell epitopes, or population coverage for vaccine candidates.
DeepMind Researcher: AGI through deep understanding, AlphaGo/AlphaZero RL, AlphaFold scientific discovery, Gemini multimodal, neuroscience-inspired architectures. Scientific rigor + industrial scale. Triggers: DeepMind research, AlphaGo algorithms, protein folding AI, scientif...
Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/environment (USGS, NOAA, EPA), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, ZINC, BindingDB), materials (Materials Project, COD), biology/genomics (Reactome, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, BioGRID, Gene Ontology, dbSNP, gnomAD, ENCODE, Human Protein Atlas, Human Cell Atlas), disease/clinical (COSMIC, Open Targets, ClinicalTrials.gov, OMIM, ClinVar, GDC/TCGA, cBioPortal, DisGeNET, GWAS Catalog), regulatory (FDA, USPTO, SEC EDGAR), economics/finance (FRED, World Bank, US Treasury), demographics (US Census, Eurostat, WHO). Use when looking up compounds, genes, proteins, pathways, variants, clinical trials, patents, economic indicators, or any public database API query.