ai4protein/venusfactory2
26 skills
$npx skills add ai4protein/venusfactory2SkillInstalls
alphafold_databaseAccess AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.arxivarXiv 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 ibiopythonComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, cubiorxivbioRxiv & 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 fobrenda_databaseAccess BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic chembl_databaseQuery ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.clustalo_msaMultiple 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,fdaQuery openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.kegg_databaseDirect REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. Use this for direct HTTP/REST work or KEGG-specific comatplotlibLow-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export nature_figureSubmission-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, figures4panature_polishingPolish, restructure, or translate academic prose into Nature-leaning English using writing-strategy principles, curated Nature/Nature Communications article patterns, and phrase-level support from Acanature_writingDraft, 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, introductncbi_clinvarQuery 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.ncbi_geneQuery 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.ncbi_sequenceNCBI 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 aopenalexOpenAlex — 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 aprotein_sequence_similarity_searchFind 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 hompubmedPubMed — 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 / biopymolHeadless 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/secrcsb_databaseRCSB 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 rdkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard wseabornStatistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pastring_databaseQuery STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.uniprot_databaseUniProt — 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,workflow_skill_creatorDistills 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"