How do I install the Brenda Database skill?

Run npx skillmds@latest add ai4protein/brenda-database in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Brenda Database safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Brenda Database?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Brenda Database free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under Unknown.

Who published Brenda Database?

ai4protein (@ai4protein) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Brenda Database by ai4protein — Agent Skill

Name: Brenda Database
Author: ai4protein

Brenda Database

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.

ai4protein 3d56524 3 files · 43.2 KB Updated Sep 17, 2026

File contents

BRENDA Database

Overview

Agent exposes download-only tools that write JSON/CSV to disk. Configure BRENDA_EMAIL + BRENDA_PASSWORD in the environment.

Project Tools (VenusFactory2)

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.

Workflow

Resolve EC number (user / UniProt / KEGG).
Pick the matching download tool; set session-scoped out_path.
Parse saved file; plot kinetics if useful (nature_figure for publication).

When NOT to use

Gene→pathway wiring without kinetics → kegg_database / string_database
Empty files usually mean missing BRENDA credentials

Common mistakes

Importing query_brenda_* as hub tools (not registered — use download_*)
Putting SOAP payloads in chat instead of reading file_info.file_path
Wrong path docs pointing at search/tools_agent.py

References (progressive disclosure)

Trust 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.

---name: brenda-databasedescription: 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---# BRENDA Database## OverviewAgent exposes **download-only** tools that write JSON/CSV to disk. Configure `BRENDA_EMAIL` + `BRENDA_PASSWORD` in the environment.## Project Tools (VenusFactory2)| 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`.## Workflow1. Resolve EC number (user / UniProt / KEGG).2. Pick the matching download tool; set session-scoped `out_path`.3. Parse saved file; plot kinetics if useful (`nature_figure` for publication).## When NOT to use- Gene→pathway wiring without kinetics → `kegg_database` / `string_database`- Empty files usually mean missing BRENDA credentials## Common mistakes- Importing `query_brenda_*` as hub tools (not registered — use `download_*`)- Putting SOAP payloads in chat instead of reading `file_info.file_path`- Wrong path docs pointing at `search/tools_agent.py`## References (progressive disclosure)**Trust order:** `SKILL.md` (hub tools & envelopes) → topic refs → `references/legacy_guide.md` (archived; may be outdated).```textread_skill(skill_id="brenda_database", relative_path="references/legacy_guide.md")```Load legacy only after the hub workflow in this file is insufficient.

Frequently asked questions