菜单
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.
默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。
决定是否安装前，请先阅读 SKILL.md，以及 SkillsMP 当前展示的配套文件。
基于 SOC 职业分类
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
直接命令不会经过审查 Prompt；运行前请先检查来源。
npx skills add https://github.com/ai4protein/VenusFactory2 --skill brenda-database命令会保持在同一行。复制前请横向滚动并检查完整内容。
想先保存到本地？可下载 SkillsMP 当前能够提供的文件。
正在显示 SKILL.md
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 mutation without labels (zero_shot_mutation_workflow) or built-in function heads already covered by predict_protein_function.
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).
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.
| name | brenda_database |
| description | 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. |
| license | Unknown |
| metadata | {"version":"1.2","skill-author":"VenusFactory2"} |
Agent exposes download-only tools that write JSON/CSV to disk. Configure BRENDA_EMAIL + BRENDA_PASSWORD in the environment.
| Tool | Key args | Purpose |
|---|---|---|
| download_brenda_km_values_by_ec_number | ec_number, out_path, optional organism/substrate | Km values |
| download_brenda_reactions_by_ec_number | ec_number, out_path | Reactions |
| download_brenda_enzymes_by_substrate | substrate, out_path, limit | Enzymes by substrate |
| download_brenda_compare_organisms_by_ec_number | ec_number, organisms, out_path | Cross-organism |
| download_brenda_environmental_parameters_by_ec_number | ec_number, out_path | pH / temperature |
| download_brenda_kinetic_data_by_ec_number | ec_number, out_path, format | Kinetic export |
| download_brenda_pathway_report | pathway (dict), out_path | Pathway report file |
Returns rich JSON with status + file_info (not {success, file_path}). Tools live in src/tools/database/tools_agent.py.
out_path.nature_figure for publication).kegg_database / string_databasequery_brenda_* as hub tools (not registered — use download_*)file_info.file_pathsearch/tools_agent.pyTrust order: SKILL.md (hub tools & envelopes) → topic refs → references/legacy_guide.md (archived; may be outdated).
read_skill(skill_id="brenda_database", relative_path="references/legacy_guide.md")
Load legacy only after the hub workflow in this file is insufficient.