Skill Claude CodeCodex
ProteinMPNN inverse folding: design or score sequences on a fixed backbone. Use when the user wants sequence design from PDB, interface/binder design, homomer symmetry, or fixed catalytic residues. Do NOT use for zero-shot mutation ranking on a wild-type sequence (zeroshotmutationworkflow) or de novo fold…
Skill Claude CodeCodex
PubMed — NCBI's biomedical literature database (>35M citations). Keyword search inline, or batch-fetch full title + structured abstract + authors + DOI for a known list of PMIDs. Use for medical / biological literature lookup, citation resolution, or building an abstract corpus for downstream NLP. Honors NCBIAPIKEY…
Skill Claude CodeCodex
Headless PyMOL rendering of protein structures (PNG + PSE session) and structural superposition with RMSD. Use to produce static publication-style images, color a structure by pLDDT/B-factor/chain/secondary-structure, or compare two structures by cealign. Do NOT use for interactive 3D exploration (use MolstarViewer in…
Skill Claude CodeCodex
RCSB Protein Data Bank (PDB) — experimentally determined 3D biomolecular structures. Search by full-text/sequence/structure/attribute, fetch entry metadata, download coordinate files (PDB/mmCIF). Use when the user provides a PDB ID, asks for structures of a protein, wants to find similar structures by sequence, or…
Skill Claude CodeCodex
RDKit cheminformatics via VenusFactory bioinfo scripts and agentgeneratedcode. Use for SMILES/SDF, descriptors, fingerprints, substructure filters, similarity. Do NOT use for ChEMBL bioactivity download (chembldatabase) or openFDA (fda). No dedicated rdkit LangChain tool — run scripts or import modules.
Skill Claude CodeCodex
Seaborn statistical plots for exploratory analysis via agentgeneratedcode. Use for quick relational/distribution/categorical charts. Do NOT use for submission-grade Nature figures (naturefigure) or low-level artists control (matplotlib).
Skill Claude CodeCodex
STRING PPI networks and enrichment via VenusFactory download tools. Use for interaction networks, partners, GO/KEGG enrichment, homology across 5000+ species. Do NOT use for sequence homology search (proteinsequencesimilaritysearch) or KEGG pathway entries alone (keggdatabase).
Skill Claude CodeCodex
Structure/sequence file preparation with VenusFactory file tools. Use for FASTA parsing, PDB chain extraction, PDB↔mmCIF conversion (MAXIT), apo checks, batch PDB→FASTA, and UniProt ID from RCSB metadata. Do NOT use for structure prediction (proteinstructurepipeline) or homology search.
Skill Claude CodeCodex
UniProt — protein sequence, function, taxonomy, cross-references. Search proteins by query, retrieve a UniProt entry, map IDs between databases (PDB↔UniProt etc.), pull FASTA sequence, fetch metadata, run SPARQL against sparql.uniprot.org. Use whenever the user mentions a UniProt accession (e.g. P04637), asks for…
Skill Claude CodeCodex
Fine-tune and run custom protein models on VenusFactory (CSV/HF → config → train → predict). Use when the user brings labeled sequences, wants adapter training (ProtT5/ESM2/Ankh/QLoRA notes), or batch inference with a trained config. Do NOT use for zero-shot mutation without labels (zeroshotmutationworkflow) or…
Skill Claude CodeCodex
Distills a completed user workflow or interaction into a reusable VenusFactory agent skill. Use when the user says "make this a skill", "create a skill from what we just did", "package this workflow" or similar. Adapts the workflow into the VenusFactory tools wiring + SKILL.md pattern. Do not use for creating skills…
Skill Claude CodeCodex
Zero-shot mutation engineering with VenusFactory PLMs. Use when the user wants beneficial mutations, directed evolution candidates, or stability/fitness ranking from a FASTA sequence or PDB structure. Do NOT use for ProteinMPNN inverse folding (proteinmpnndesignworkflow), sequence homology search…