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AlphaFold Structure Access

alphafold-database

K-Dense-AI/claude-scientific-skills

Retrieve AlphaFold’s AI-predicted protein models via UniProt IDs, download CIF/PDB coordinates, inspect confidence metrics, and feed them into structural analysis or drug-discovery pipelines.

bioRxiv Preprint Search

biorxiv-database

K-Dense-AI/claude-scientific-skills

Enables efficient querying of the bioRxiv preprint server with keywords, authors, dates, and categories, returning structured JSON metadata and optional PDF downloads for literature reviews or tracking research trends.

ClinVar Variant Explorer

clinvar-database

K-Dense-AI/claude-scientific-skills

Query NCBI ClinVar for variant clinical significance, mixing gene/condition searches, API/FTP downloads, and VCF annotations to support genomic medicine interpretation workflows.

COSMIC Mutation Access

cosmic-database

K-Dense-AI/claude-scientific-skills

Programmatic access to the COSMIC cancer mutation database for downloading mutations, Cancer Gene Census, mutational signatures, fusions, copy number, expression, and resistance data to fuel oncology research or bioinformatics pipelines after authentication.

DrugBank Database Insights

drugbank-database

K-Dense-AI/claude-scientific-skills

Provides programmatic access to DrugBank drug and target data, covering downloads, queries, interaction networks, targets/pathways, and chemical similarity analyses for pharmacology research and safety reviews.

GEO Data Retriever

K-Dense-AI/claude-scientific-skills

Connect to NCBI's GEO repository, search series/samples/platforms via Entrez queries, fetch profiles, and download raw/processed matrices using GEOparse for transcriptomics and expression analysis workflows.

GWAS Catalog Access

K-Dense-AI/claude-scientific-skills

Query the NHGRI-EBI GWAS Catalog for SNP-trait associations, fetch study metadata, variant and trait details, and download summary statistics via the web or REST APIs to support genetic epidemiology and polygenic risk modeling.

Human Metabolome Explorer

K-Dense-AI/claude-scientific-skills

Access HMDB to search over 220K human metabolites by name, ID, structure, disease or specimen, retrieve chemical/clinical/pathway data, and download spectra for metabolomics workflows.

Cancer Imaging Data Access

imaging-data-commons

K-Dense-AI/claude-scientific-skills

Query and download the NCI Imaging Data Commons public cancer imaging datasets via idc-index, filter by metadata, fetch DICOM files, visualize series, and respect licensing details for AI training or research.

PDB Structure Explorer

K-Dense-AI/claude-scientific-skills

Access RCSB PDB to search biomolecular structures via text, sequence, or geometry queries, download coordinate files in PDB/mmCIF/Binary formats, retrieve metadata, and batch-process entries for drug discovery, protein engineering, and structural biology pipelines.

BindingDB Affinity Access

bindingdb-database

K-Dense-AI/claude-scientific-skills

Query BindingDB for measured drug-target affinities (Ki, Kd, IC50, EC50) via REST endpoints or downloaded TSVs to support target-centric drug discovery, SAR analysis, lead profiling, and benchmarking datasets.

DepMap Dependency Explorer

K-Dense-AI/claude-scientific-skills

Access DepMap data to fetch CRISPR Chronos dependency scores, drug sensitivity readouts, and gene effect profiles for cancer cell lines, supporting target validation, biomarker discovery, and synthetic-lethality research via API or downloads.

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