diff --git a/.claude-plugin/marketplace.json b/.claude-plugin/marketplace.json index 5dbee73..a5614c2 100644 --- a/.claude-plugin/marketplace.json +++ b/.claude-plugin/marketplace.json @@ -7,7 +7,7 @@ }, "metadata": { "description": "Claude scientific skills from K-Dense Inc", - "version": "2.7.0" + "version": "2.8.0" }, "plugins": [ { @@ -106,6 +106,7 @@ "./scientific-skills/fda-database", "./scientific-skills/gene-database", "./scientific-skills/generate-image", + "./scientific-skills/brenda-database", "./scientific-skills/geo-database", "./scientific-skills/gwas-database", "./scientific-skills/hmdb-database", diff --git a/README.md b/README.md index c7d1f1d..0b434a3 100644 --- a/README.md +++ b/README.md @@ -415,7 +415,7 @@ This repository contains **123+ scientific skills** organized across multiple do - Publishing: Paper-2-Web - Illustration: Generate Image (AI image generation with FLUX.2 Pro and Gemini 3 Pro) -#### 🔬 **Scientific Databases** (26+ skills) +#### 🔬 **Scientific Databases** (27+ skills) - Protein: UniProt, PDB, AlphaFold DB - Chemical: PubChem, ChEMBL, DrugBank, ZINC, HMDB - Genomic: Ensembl, NCBI Gene, GEO, ENA, GWAS Catalog @@ -423,6 +423,7 @@ This repository contains **123+ scientific skills** organized across multiple do - Pathways: KEGG, Reactome, STRING - Targets: Open Targets - Metabolomics: Metabolomics Workbench +- Enzymes: BRENDA - Patents: USPTO #### 🔧 **Infrastructure & Platforms** (5+ skills) diff --git a/docs/scientific-skills.md b/docs/scientific-skills.md index 8ebb04c..6f0f603 100644 --- a/docs/scientific-skills.md +++ b/docs/scientific-skills.md @@ -3,6 +3,7 @@ ## Scientific Databases - **AlphaFold DB** - Comprehensive AI-predicted protein structure database from DeepMind providing 200M+ high-confidence protein structure predictions covering UniProt reference proteomes and beyond. Includes confidence metrics (pLDDT for per-residue confidence, PAE for pairwise accuracy estimates), structure quality assessment, predicted aligned error matrices, and multiple structure formats (PDB, mmCIF, AlphaFold DB format). Supports programmatic access via REST API, bulk downloads through Google Cloud Storage, and integration with structural analysis tools. Enables structure-based drug discovery, protein function prediction, structural genomics, comparative modeling, and structural bioinformatics research without experimental structure determination +- **BRENDA** - World's most comprehensive enzyme information system containing detailed enzyme data from scientific literature. Query kinetic parameters (Km, kcat, Vmax), reaction equations, substrate specificities, organism information, and optimal conditions for 45,000+ enzymes with millions of kinetic data points via SOAP API. Supports enzyme discovery by substrate/product, cross-organism comparisons, environmental parameter analysis (pH, temperature optima), cofactor requirements, inhibition/activation data, and thermophilic homolog identification. Includes helper scripts for parsing BRENDA response formats, visualization of kinetic parameters, and enzymatic pathway construction. Use cases: metabolic engineering, enzyme engineering and optimization, kinetic modeling, retrosynthesis planning, industrial enzyme selection, and biochemical research requiring comprehensive enzyme kinetic data - **ChEMBL** - Comprehensive manually curated database of bioactive molecules with drug-like properties maintained by EMBL-EBI. Contains 2M+ unique compounds, 19M+ bioactivity measurements, 13K+ protein targets, and 1.1M+ assays from 90K+ publications. Provides detailed compound information including chemical structures (SMILES, InChI), bioactivity data (IC50, EC50, Ki, Kd values), target information (protein families, pathways), ADMET properties, drug indications, clinical trial data, and patent information. Features REST API access, web interface, downloadable data files, and integration with other databases (UniProt, PubChem, DrugBank). Use cases: drug discovery, target identification, lead optimization, bioactivity prediction, chemical biology research, and drug repurposing - **ClinPGx** - Clinical pharmacogenomics database (successor to PharmGKB) providing gene-drug interactions, CPIC clinical guidelines, allele functions, drug labels, and pharmacogenomic annotations for precision medicine and personalized pharmacotherapy (consolidates PharmGKB, CPIC, and PharmCAT resources) - **ClinVar** - NCBI's public archive of genomic variants and their clinical significance with standardized classifications (pathogenic, benign, VUS), E-utilities API access, and bulk FTP downloads for variant interpretation and precision medicine research