VenusFactory2

In the author's own words, from each skill's SKILL.md — showing the first 30 of 36 files.

• alphafold_database

  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 (rcsb_database), local ESMFold without UniProt (predict_structure_esmfold / protein_structure_pipeline), or sequence annotation (uniprot_database).

  src/agent/skills/alphafold_database/SKILL.md on GitHub (opens in a new tab)

• arxiv

  arXiv preprint server — keyword search the official API and download papers as PDF / HTML / source tarball. Use whenever the user mentions an arXiv ID (e.g. 2106.04559) or wants preprints on a topic in CS / physics / math / quantitative biology. For biomedical preprints specifically, prefer biorxiv skill.

  src/agent/skills/arxiv/SKILL.md on GitHub (opens in a new tab)

• biopython

  Biopython guidance for sequence I/O, alignments, Bio.PDB, and Entrez parsing. Use for custom bioinformatics code via agent_generated_code. Prefer VenusFactory download tools for NCBI/UniProt/AlphaFold bulk fetches so large payloads stay on disk. Do NOT use as a substitute for protein_sequence_similarity_search or alphafold_database hub tools.

  src/agent/skills/biopython/SKILL.md on GitHub (opens in a new tab)

• biorxiv

  bioRxiv & medRxiv — biology / medicine preprint servers. Search by keyword + date window, fetch a specific preprint's full metadata (with all version history + abstract + JATS XML link) by DOI. Use for cutting-edge biology/medicine work that hasn't gone through peer review yet, or to find the original preprint version of a paper you only have the DOI for.

  src/agent/skills/biorxiv/SKILL.md on GitHub (opens in a new tab)

• brenda_database

  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 (kegg_database) or protein sequence fetch (uniprot_database). Requires BRENDA_EMAIL and BRENDA_PASSWORD.

  src/agent/skills/brenda_database/SKILL.md on GitHub (opens in a new tab)

• chembl_database

  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).

  src/agent/skills/chembl_database/SKILL.md on GitHub (opens in a new tab)

• clustalo_msa

  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 protein_sequence_similarity_search), structural alignment (use foldseek), or DNA/RNA alignment.

  src/agent/skills/clustalo_msa/SKILL.md on GitHub (opens in a new tab)

• fda

  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 (chembl_database) or general biomedical literature (pubmed).

  src/agent/skills/fda/SKILL.md on GitHub (opens in a new tab)

• foldseek_structural_similarity

  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 (protein_sequence_similarity_search) or MSA (clustalo_msa).

  src/agent/skills/foldseek_structural_similarity/SKILL.md on GitHub (opens in a new tab)

• hpa_expression_context

  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 (string_database).

  src/agent/skills/hpa_expression_context/SKILL.md on GitHub (opens in a new tab)

• interpro_domain_annotation

  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 (string_database / kegg_database) or kinetic parameters (brenda_database).

  src/agent/skills/interpro_domain_annotation/SKILL.md on GitHub (opens in a new tab)

• kegg_database

  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 (string_database) or enzyme kinetics (brenda_database). Non-academic use of KEGG requires a commercial license.

  src/agent/skills/kegg_database/SKILL.md on GitHub (opens in a new tab)

• matplotlib

  Matplotlib OO/pyplot guidance for custom plots via agent_generated_code. Use for fine-grained control. Prefer nature_figure for manuscript figures and seaborn for quick statistical EDA.

  src/agent/skills/matplotlib/SKILL.md on GitHub (opens in a new tab)

• nature_figure

  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 journals. Before plotting, define the figure's conclusion, evidence logic, export…

  src/agent/skills/nature_figure/SKILL.md on GitHub (opens in a new tab)

• nature_polishing

  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, discussion, conclusion, title, methods section, or Chinese academic draft for publicati…

  src/agent/skills/nature_polishing/SKILL.md on GitHub (opens in a new tab)

• nature_writing

  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 polish finished prose. Also trigger on general academic-writing requests even witho…

  src/agent/skills/nature_writing/SKILL.md on GitHub (opens in a new tab)

• ncbi_clinvar

  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.

  src/agent/skills/ncbi_clinvar/SKILL.md on GitHub (opens in a new tab)

• ncbi_gene

  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.

  src/agent/skills/ncbi_gene/SKILL.md on GitHub (opens in a new tab)

• ncbi_sequence

  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. Don't use for ClinVar variants (use ncbi_clinvar) or gene metadata lookup (us…

  src/agent/skills/ncbi_sequence/SKILL.md on GitHub (opens in a new tab)

• openalex

  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 publications, institution outputs, or research topics. Lower-friction alternative to…

  src/agent/skills/openalex/SKILL.md on GitHub (opens in a new tab)

• protein_engineering_hypothesis

  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 model scores as hypotheses.

  src/agent/skills/protein_engineering_hypothesis/SKILL.md on GitHub (opens in a new tab)

• protein_property_prediction

  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 (zero_shot_mutation_workflow) or custom model training (train tools / future finetune workflow).

  src/agent/skills/protein_property_prediction/SKILL.md on GitHub (opens in a new tab)

• protein_sequence_similarity_search

  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 foldseek) or DNA/RNA queries.

  src/agent/skills/protein_sequence_similarity_search/SKILL.md on GitHub (opens in a new tab)

• protein_structure_pipeline

  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 (zero_shot_mutation_workflow), FoldSeek search (foldseek_structural_similarity), or experimental PDB-only metadata without structure needs (rcsb_database alone may su…

  src/agent/skills/protein_structure_pipeline/SKILL.md on GitHub (opens in a new tab)

• proteinmpnn_design_workflow

  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 (zero_shot_mutation_workflow) or de novo fold hallucination without a backbone.

  src/agent/skills/proteinmpnn_design_workflow/SKILL.md on GitHub (opens in a new tab)

• pubmed

  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 NCBI_API_KEY env var.

  src/agent/skills/pubmed/SKILL.md on GitHub (opens in a new tab)

• pymol

  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 the frontend), docking, MD simulation, or sequence-only analysis.

  src/agent/skills/pymol/SKILL.md on GitHub (opens in a new tab)

• rcsb_database

  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 needs experimental (not predicted) coordinates. Don't use for AlphaFold predictions…

  src/agent/skills/rcsb_database/SKILL.md on GitHub (opens in a new tab)

• rdkit

  RDKit cheminformatics via VenusFactory bioinfo scripts and agent_generated_code. Use for SMILES/SDF, descriptors, fingerprints, substructure filters, similarity. Do NOT use for ChEMBL bioactivity download (chembl_database) or openFDA (fda). No dedicated rdkit_* LangChain tool — run scripts or import modules.

  src/agent/skills/rdkit/SKILL.md on GitHub (opens in a new tab)

• seaborn

  Seaborn statistical plots for exploratory analysis via agent_generated_code. Use for quick relational/distribution/categorical charts. Do NOT use for submission-grade Nature figures (nature_figure) or low-level artists control (matplotlib).

  src/agent/skills/seaborn/SKILL.md on GitHub (opens in a new tab)

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