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SkillsMP has collected 36 skills from ai4protein/VenusFactory2. Open a skill to review its source and details.
Showing 36 of 36 collected skills.
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:…
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…
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…
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…
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 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…
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.
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…
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…
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,…
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.
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.
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…
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…
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…
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.…
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…
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…
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…
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…
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…
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…
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…
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).
STRING PPI networks and enrichment via VenusFactory download tools. Use for interaction networks, partners, GO/KEGG enrichment, homology across 5000+ species. Do NOT use for sequence homology search (protein_sequence_similarity_search) or KEGG pathway entries…
Structure/sequence file preparation with VenusFactory file tools. Use for FASTA parsing, PDB chain extraction, PDB↔mmCIF conversion (MAXIT), apo checks, batch PDB→FASTA, and UniProt ID from RCSB metadata. Do NOT use for structure prediction…
UniProt — 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, run SPARQL against sparql.uniprot.org. Use whenever the…
Distills 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" or similar. Adapts the workflow into the VenusFactory tools…
Zero-shot mutation engineering with VenusFactory PLMs. Use when the user wants beneficial mutations, directed evolution candidates, or stability/fitness ranking from a FASTA sequence or PDB structure. Do NOT use for ProteinMPNN inverse folding…