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…
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…
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…
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…
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…
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…
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).
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:…