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Adaptyv Bio Foundry API

K-Dense-AI/claude-scientific-skills

Guides use of the Adaptyv Bio Foundry API and Python SDK to design protein experiments, submit sequences, automate workflows, and fetch BLI/SPR or thermostability assay results via authenticated requests for lab-ready studies.

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.

Annotated Data Matrix

K-Dense-AI/claude-scientific-skills

AnnData supplies a Python-native container for annotated matrices, letting researchers store measurements alongside rich metadata, read/write h5ad/zarr/loom/10X files, and integrate with the scverse tools when building single-cell or related data workflows.

Benchling Integration Toolkit

benchling-integration

K-Dense-AI/claude-scientific-skills

Automate Benchling lab data workflows via the Python SDK or REST API: manage registry entities (DNA, proteins), inventory, ELN entries, workflows, and Data Warehouse queries for syncing and analytics.

BGPT Structured Paper Search

bgpt-paper-search

K-Dense-AI/claude-scientific-skills

BGPT Paper Search queries the remote MCP server to retrieve structured experimental data from full-text studies, returning methods, results, sample sizes, quality scores, and conclusions for efficient literature reviews and evidence synthesis.

Cirq Quantum Toolkit

K-Dense-AI/claude-scientific-skills

Cirq is Google Quantum AI’s Python framework for building, simulating, and deploying noise-aware quantum circuits on both simulators and real hardware, complete with experiment templates, transformation utilities, and hardware-specific toolkits.

Clinical Report Composer

clinical-reports

K-Dense-AI/claude-scientific-skills

Compose comprehensive clinical reports—case studies, diagnostics, trials, and patient notes—while ensuring CARE/ICH-GCP compliance, HIPAA-safe documentation, and mandatory AI-generated scientific schematics for each deliverable.

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.

DiffDock Pose Predictor

K-Dense-AI/claude-scientific-skills

DiffDock uses diffusion-based deep learning to predict protein-ligand binding poses, confidence, and batch virtual screening workflows for structure-based drug design.

ENA Sequence Access

K-Dense-AI/claude-scientific-skills

Access the European Nucleotide Archive via REST/FTP to fetch DNA/RNA sequences, raw reads, assemblies, annotations, and taxonomy for research or bioinformatics pipelines.

Ensembl Genome API

ensembl-database

K-Dense-AI/claude-scientific-skills

Query Ensembl’s RESTful API to access gene annotations, sequences, variants, orthologs, and assembly mappings across 250+ species, enabling integration into genomic research pipelines.

ESM Protein Modeling Toolkit

K-Dense-AI/claude-scientific-skills

Combines ESM3 and ESM C protein language models to generate sequences, predict structures, condition functions, and extract embeddings via local or Forge API inference for protein design and engineering workflows.

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