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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.

PubMed Database Access

pubmed-database

K-Dense-AI/claude-scientific-skills

Direct REST/API access to PubMed for constructing complex Boolean or MeSH queries, filtering by publication attributes, and automating literature retrieval or citation management via NCBI’s E-utilities.

Reactome Pathway Explorer

reactome-database

K-Dense-AI/claude-scientific-skills

Query the Reactome Content and Analysis Services (or the reactome2py client) to fetch pathway hierarchies, map genes, run overrepresentation/expression analyses, and explore disease interactions for systems biology research.

STRING Protein Interaction

string-database

K-Dense-AI/claude-scientific-skills

Query the STRING REST API to retrieve protein-protein interaction networks, map identifiers, visualize evidence-weighted edges, and run GO/KEGG/Pfam enrichment for systems biology analysis.

UniProt Rest Access

uniprot-database

K-Dense-AI/claude-scientific-skills

Direct REST API access to UniProt for searching proteins, fetching FASTA sequences, mapping identifiers, selecting annotations, and streaming large datasets within Python workflows.

Zinc Compound Access

K-Dense-AI/claude-scientific-skills

Query UCSF’s ZINC22 repository of 230M+ purchasable compounds via the web UI or CartBlanche APIs to fetch IDs/SMILES, run similarity, supplier, or random sampling, and assemble docking-ready libraries for virtual screening.

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.

cBioPortal Cancer Data

cbioportal-database

K-Dense-AI/claude-scientific-skills

Access multi-dimensional cancer genomics data via cBioPortal REST API for mutation, copy-number, expression, and survival insights across TCGA/GENIE studies, enabling target validation and clinical association analyses programmatically with Python clients.

GnomAD Variant Lookup

gnomad-database

K-Dense-AI/claude-scientific-skills

Query gnomAD via GraphQL to retrieve allele frequencies, constraint scores, and loss-of-function annotations for population-informed variant interpretation and rare disease gene prioritization.

GTEx Expression Explorer

K-Dense-AI/claude-scientific-skills

Query the GTEx portal and API to retrieve tissue-specific gene expression, eQTL, sQTL, and variant-level regulatory data for interpreting GWAS loci and exploring gene regulation across 54 human tissues.

InterPro Protein Annotation

interpro-database

K-Dense-AI/claude-scientific-skills

Query InterPro for protein family, domain, and GO annotations via a REST API with Python helpers, enabling function prediction, domain architecture mapping, and evolutionary classification insights for proteomic workflows.

Jaspar TFBS Toolkit

jaspar-database

K-Dense-AI/claude-scientific-skills

Query the JASPAR REST API and Python helpers to retrieve TF binding profiles, convert PFMs to PWMs, and scan DNA sequences for high-confidence motifs, enabling regulatory variant interpretation, ChIP/ATAC analysis, and TF network construction.

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