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Search Protein , found 32 results

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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.

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.

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.

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.

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.

PyOpenMS Mass Spectrometry

K-Dense-AI/claude-scientific-skills

PyOpenMS provides Python bindings for OpenMS to drive complete mass spectrometry workflows, covering data IO, spectral processing, feature/peptide-protein identification, quantitation, and metabolomics pipelines.

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.

TorchDrug GNN Toolkit

K-Dense-AI/claude-scientific-skills

TorchDrug is a PyTorch-native toolbox for building graph neural networks tailored to molecules, proteins, and biomedical knowledge graphs, covering property prediction, generation, retrosynthesis, and knowledge graph reasoning with curated datasets and models.

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.

Ginkgo Cloud Lab Automation

ginkgo-cloud-lab

K-Dense-AI/claude-scientific-skills

Submit and manage autonomous lab protocols on Ginkgo Cloud Lab, leveraging RACs for cell-free protein expression validation/optimization, fluorescent pixel art, EstiMate AI assessments, and guided ordering of sample inputs through the web interface.

Glycoengineering Toolkit

glycoengineering

K-Dense-AI/claude-scientific-skills

Analyzes protein sequences to locate canonical N-glycosylation sequons, predict O-glycosylation hotspots, and mutate or design glycosylation sites for therapeutic proteins, vaccines, and biosimilar comparisons using curated glycoengineering resources.

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