Skill Claude CodeCodex
AlphaFold DB structures and confidence analytics via VenusFactory tools. Use when the user needs predicted structures by UniProt ID, pLDDT/PAE analysis, or PDB/mmCIF download. Do NOT use for experimental PDB (rcsbdatabase), local ESMFold without UniProt (predictstructureesmfold / proteinstructurepipeline), or sequence…
Skill Claude CodeCodex
Two complementary tools: queryarxiv (text search, returns JSON list inline) + downloadarxivpaperbyid (fetches the actual paper as PDF / HTML / source tarball to disk).
Skill Claude CodeCodex
Biopython guidance for sequence I/O, alignments, Bio.PDB, and Entrez parsing. Use for custom bioinformatics code via agentgeneratedcode. Prefer VenusFactory download tools for NCBI/UniProt/AlphaFold bulk fetches so large payloads stay on disk. Do NOT use as a substitute for proteinsequencesimilaritysearch or…
Skill Claude CodeCodex
Two tools: existing querybiorxivtool (keyword/category date-window search) + new downloadbiorxivbydoi (fetch one preprint by DOI with all metadata, including version history).
Skill Claude CodeCodex
BRENDA enzyme kinetics via VenusFactory download tools (SOAP). Use for Km/kcat, reactions, organism comparison, environmental optima by EC number. Do NOT use for pathway maps alone (keggdatabase) or protein sequence fetch (uniprotdatabase). Requires BRENDAEMAIL and BRENDAPASSWORD.
Skill Claude CodeCodex
ChEMBL bioactive molecules and drugs via VenusFactory download tools. Use for molecule/drug by ID, similarity/substructure by SMILES, SAR starting points. Do NOT use for openFDA regulatory data (fda) or RDKit-only local chemistry (rdkit).
Skill Claude CodeCodex
Multiple sequence alignment of proteins via EBI Clustal Omega web service. Use when you have ≥2 protein sequences in a FASTA file (≤4000 sequences, ≤4 MB) and need an alignment to assess conservation, residue importance, or domain structure. Do NOT use for: single sequences, homology search (use…
Skill Claude CodeCodex
Query openFDA via VenusFactory for drugs, devices, adverse events, recalls, and regulatory submissions (510k, PMA). Use when the user needs FDA pharmacovigilance, labeling, NDC/UNII, or openFDA analytics. Do NOT use for ChEMBL bioactivity (chembldatabase) or general biomedical literature (pubmed).
Skill Claude CodeCodex
FoldSeek structural similarity search against PDB with optional protected-region masking. Use when the user has a PDB and wants fold-level homologs, structural neighbors, or to protect an active site while searching. Do NOT use for sequence BLAST/MMseqs2 (proteinsequencesimilaritysearch) or MSA (clustalomsa).
Skill Claude CodeCodex
Human Protein Atlas expression and localization via VenusFactory download tools. Use when the user needs tissue expression, subcellular location, single-cell type, blood expression, or protein summary by gene symbol for therapeutic/target context. Do NOT use for mouse/non-human expression atlases or PPI networks…
Skill Claude CodeCodex
InterPro domain/family annotation via VenusFactory download tools. Use when the user needs domain boundaries, family membership, or UniProt→InterPro annotations for engineering target selection. Do NOT use for pathway enrichment (stringdatabase / keggdatabase) or kinetic parameters (brendadatabase).
Skill Claude CodeCodex
KEGG REST access via VenusFactory download tools (academic use). Use for pathway/gene/compound lookups, ID conversion, and DDI. Do NOT use for PPI networks (stringdatabase) or enzyme kinetics (brendadatabase). Non-academic use of KEGG requires a commercial license.
Skill Claude CodeCodex
Matplotlib OO/pyplot guidance for custom plots via agentgeneratedcode. Use for fine-grained control. Prefer naturefigure for manuscript figures and seaborn for quick statistical EDA.
Skill Claude CodeCodex
Submission-grade Nature/high-impact journal figure workflow for Python or R. Use whenever the user asks to create, revise, audit, or polish manuscript figures, multi-panel scientific plots, figures4papers-style matplotlib plots, or journal-ready SVG/PDF/TIFF outputs, especially for Nature-family or other high-impact…
Skill Claude CodeCodex
Polish, restructure, or translate academic prose into Nature-leaning English using writing-strategy principles, curated Nature/Nature Communications article patterns, and phrase-level support from Academic Phrasebank. Use whenever the user asks to polish a manuscript paragraph, abstract, introduction, results…
Skill Claude CodeCodex
Draft, restructure, or plan Nature-style manuscript sections from author-provided claims, results, figures, notes, or Chinese drafts. Use when the user wants to write or rebuild an abstract, introduction, related-work, method, experiments, discussion, conclusion, title, or full manuscript argument rather than only…
Skill Claude CodeCodex
Query NCBI ClinVar for variant clinical significance. Search by gene/condition/CLNSIG, interpret pathogenicity, use E-utilities or FTP; annotate VCFs. Use project tools in src.tools.database.ncbi.
Skill Claude CodeCodex
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
Skill Claude CodeCodex
NCBI E-utilities for biological sequences — fetch protein/nucleotide FASTA by accession, run BLAST, translate CDS to protein, search NCBI Protein by gene+organism. Use when the user provides an NCBI accession (NP, XP, NM, NR, etc.), asks for a sequence by gene name + species, or needs to translate a coding sequence.…
Skill Claude CodeCodex
OpenAlex — free, comprehensive scholarly graph (works, authors, sources/journals, institutions, topics, concepts, funders). Search papers by keyword/filter/sort, fetch a single entity by ID, look up author profiles, institutions, citation networks. Use whenever the user asks about papers, citation counts, author…
Skill Claude CodeCodex
Evidence-bounded hypothesis and experiment planning for protein engineering. Use when the user asks what to mutate next, how to prioritize variants, how to falsify a mechanism, or how to design a directed-evolution round. Do NOT invent wet-lab results; chain VenusFactory tools for computational evidence and label…
Skill Claude CodeCodex
Physicochemical properties, surface/SS features, and finetuned protein/residue function prediction. Use when the user asks for solubility, optimal temperature, activity/binding/conserved sites, RSA/SASA/secondary structure, or property tables from FASTA/PDB. Do NOT use for zero-shot mutation ranking…
Skill Claude CodeCodex
Find homologous protein sequences from a query sequence using MMseqs2 (fast, ColabFold web API) or BLAST (comprehensive, EBI). Use when the user provides a protein sequence or FASTA file and wants homologs, function inference by sequence similarity, or input for an MSA. Do NOT use for structural similarity (use…
Skill Claude CodeCodex
Protein structure obtain → confidence → visualize pipeline. Use when the user needs a 3D structure from sequence or UniProt ID, AlphaFold/ESMFold retrieval, pLDDT/PAE analysis, or structure rendering. Do NOT use for mutation ranking (zeroshotmutationworkflow), FoldSeek search (foldseekstructuralsimilarity), or…