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Found 21 Skills
Guidance for designing fusion protein gBlock sequences from multiple protein sources. This skill applies when tasks involve combining proteins from PDB databases, plasmid files, and fluorescent protein databases into a single optimized DNA sequence with specific linkers and codon optimization requirements.
Search and analyze cryo-EM maps, single particle structures, tomography datasets, and raw micrograph data from EMDB, EMPIAR, and CryoET Data Portal. Cross-reference with PDB structures and AlphaFold predictions. Use for cryo-EM map discovery, structure fitting analysis, raw data access, and tomography exploration.
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.
MSVC cl.exe and clang-cl skill for Windows C/C++ projects. Use when configuring Visual Studio builds, MSBuild, or clang-cl as a drop-in MSVC replacement. Covers translating GCC/Clang flags to MSVC equivalents, runtime library selection, Windows SDK setup, and diagnosing MSVC-specific errors. Activates on queries about cl.exe, clang-cl, /O flags, /MT vs /MD, PDB files, Windows ABI, or MSVC project settings.
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.
Systematic clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Aggregates evidence from ClinVar, gnomAD, CIViC, UniProt, and PDB across ACMG criteria. Produces pathogenicity scores (0-100), clinical recommendations, and treatment implications. Use when interpreting genetic variants, classifying variants of uncertain significance (VUS), performing ACMG variant classification, or translating variant calls to clinical actionability.
Debug Django web applications with systematic diagnostic approaches. This skill covers troubleshooting Django-specific errors including TemplateDoesNotExist, ImproperlyConfigured, IntegrityError, migration conflicts, CSRF failures, N+1 query problems, and circular imports. Includes Django Debug Toolbar setup, ORM query logging, pdb/ipdb usage, shell_plus debugging, and comprehensive logging configuration. Provides four-phase methodology for root cause analysis and regression prevention.
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.
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.