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),…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.biopythonComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access…biorxivbioRxiv & medRxiv — biology / medicine preprint servers. Search by keyword + date window, fetch a specific preprint's full metadata (with all version history +…brenda_databaseAccess BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme…chembl_databaseQuery ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors,…clustalo_msaMultiple sequence alignment of proteins via EBI Clustal Omega web service.fdaQuery openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data…kegg_databaseDirect REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion.matplotlibLow-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating…nature_figureSubmission-grade Nature/high-impact journal figure workflow for Python or R.nature_polishingnature_writingDraft, restructure, or plan Nature-style manuscript sections from author-provided claims, results, figures, notes, or Chinese drafts.ncbi_clinvarQuery NCBI ClinVar for variant clinical significance. Search by gene/condition/CLNSIG, interpret pathogenicity, use E-utilities or FTP; annotate VCFs.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…ncbi_sequenceNCBI E-utilities for biological sequences — fetch protein/nucleotide FASTA by accession, run BLAST, translate CDS to protein, search NCBI Protein by…openalexOpenAlex — free, comprehensive scholarly graph (works, authors, sources/journals, institutions, topics, concepts, funders).protein_sequence_similarity_searchFind homologous protein sequences from a query sequence using MMseqs2 (fast, ColabFold web API) or BLAST (comprehensive, EBI).pubmedPubMed — NCBI's biomedical literature database (>35M citations).pymolHeadless PyMOL rendering of protein structures (PNG + PSE session) and structural superposition with RMSD.rcsb_databaseRCSB Protein Data Bank (PDB) — experimentally determined 3D biomolecular structures.rdkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D…seabornStatistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive…string_databaseQuery STRING API for protein-protein interactions (59M proteins, 20B interactions).uniprot_databaseUniProt — protein sequence, function, taxonomy, cross-references.workflow_skill_creatorDistills a completed user workflow or interaction into a reusable VenusFactory agent skill.