Bio Structural Biology Structure Navigation
GPTomics/bioSkills
Navigate the Bio.PDB SMCRA hierarchy (Structure-Model-Chain-Residue-Atom) safely, surfacing the heterogeneity it hides by default.
Give agents persistent structural memory of a codebase — navigate dependencies, track public APIs, and understand why connections exist without re-reading the whole repo.
No licenceAuto-check passed
Install Data Structure Protocol
$ npx skills add aiskillstore/marketplace --skill data-structure-protocol -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aiskillstore/marketplace data-structure-protocol --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/sickn33/data-structure-protocol .claude/skills/data-structure-protocol && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "data-structure-protocol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/sickn33/data-structure-protocol into .claude/skills/data-structure-protocol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-structure-protocol", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/aiskillstore/marketplace/tree/main/skills/sickn33/data-structure-protocolType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add aiskillstore/marketplace --skill data-structure-protocol -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aiskillstore/marketplace data-structure-protocol --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/sickn33/data-structure-protocol .agents/skills/data-structure-protocol && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "data-structure-protocol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/sickn33/data-structure-protocol into .agents/skills/data-structure-protocol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-structure-protocol", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aiskillstore/marketplace --skill data-structure-protocol -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aiskillstore/marketplace data-structure-protocol --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/sickn33/data-structure-protocol .cursor/skills/data-structure-protocol && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "data-structure-protocol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/sickn33/data-structure-protocol into .cursor/skills/data-structure-protocol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-structure-protocol", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/aiskillstore/marketplace.git --path skills/sickn33/data-structure-protocol--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add aiskillstore/marketplace --skill data-structure-protocol -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aiskillstore/marketplace data-structure-protocol --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/sickn33/data-structure-protocol .gemini/skills/data-structure-protocol && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "data-structure-protocol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/sickn33/data-structure-protocol into .gemini/skills/data-structure-protocol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-structure-protocol", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install aiskillstore/marketplace data-structure-protocolInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add aiskillstore/marketplace --skill data-structure-protocol -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/sickn33/data-structure-protocol .github/skills/data-structure-protocol && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "data-structure-protocol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/sickn33/data-structure-protocol into .github/skills/data-structure-protocol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-structure-protocol", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aiskillstore/marketplace --skill data-structure-protocol -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aiskillstore/marketplace data-structure-protocol --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/sickn33/data-structure-protocol .opencode/skills/data-structure-protocol && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "data-structure-protocol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/sickn33/data-structure-protocol into .opencode/skills/data-structure-protocol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "data-structure-protocol", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
data-structure-protocol- GitHub stars
- 430
- Used in
- 3 other repos
- Token cost
- ~2.5k tokens
- SKILL.md length
- 925 words
- Files
- 2
- Skills in repo
- 1,085
- Repo updated
- First seen
- Licence
- None found
At a glance
Give agents persistent structural memory of a codebase — navigate dependencies, track public APIs, and understand why connections exist without re-reading the whole repo.
- Works in 5 steps: Identify root entrypoints (package.json… → Document the root file: create-object,… → Take the first non-external import,… → …
- SKILL.md covers When to Use, Core Concepts, How It Works and Examples, plus 4 more sections
- Calls python and curl; reaches raw.githubusercontent.com
What it does
Data Structure Protocol is an agent skill from aiskillstore/marketplace. Give agents persistent structural memory of a codebase — navigate dependencies, track public APIs, and understand why connections exist without re-reading the whole repo.
Its SKILL.md is about 2.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `skill-report.json`).
The repository describes itself as: Security-audited skills for Claude, Codex & Claude Code. One-click install, quality verified.
Example prompts
- “/data-structure-protocol”
Requirements
- Python 3
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Identify root entrypoints (package.json main, framework entry, main.py, etc.)
- Document the root file: create-object, create-function for each export, create-shared, add-import for all dependencies
- Take the first non-external import, document it fully, descend into its imports
- Backtrack when no unvisited local imports remain; continue until all reachable files are documented
- External dependencies: create-object --kind external, add to TOC, but never descend into node_modules/site-packages/etc.
What it can do on your machine
Read from SKILL.md and the folder at commit 4ac52da. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
pythoncurl
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
raw.githubusercontent.com
Also links to:
github.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Data Structure Protocol loads about 2.5k tokens when it runs. Until then it costs about 49 tokens; SKILL.md has 925 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 925 words (~2,457 tokens).
“LLM coding agents lose context between tasks. On large codebases they spend most of their tokens on "orientation" — figuring out where things live, what depends on what, and what is safe to change. DSP solves this by externalizing the…”
- name
- data-structure-protocol
- risk
- safe
- source
- https://github.com/k-kolomeitsev/data-structure-protocol
- date_added
- 2026-02-27
Files
SKILL.md and 1 other file in skills/sickn33/data-structure-protocol of aiskillstore/marketplace.
- SKILL.md
- skill-report.json
Open the folder on GitHubat commit 4ac52da
Used in 3 other repositories
We found 12 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 3 other GitHub owners. This page covers the copy in aiskillstore/marketplace, which our catalogue first saw on October 7, 2026.
- sickn33/agentic-awesome-skillsskills/data-structure-protocolplugins/agentic-awesome-skills/skills/data-structure-protocol+1 more
- lingxling/awesome-skills-cnantigravity-awesome-skills/skills/data-structure-protocolantigravity-awesome-skills/plugins/agentic-awesome-skills/skills/data-structure-protocol+1 more
- henryalouf/ruflow.agents/skills/data-structure-protocol.agents/skills/antigravity-awesome-skills/skills/data-structure-protocol+4 more
Compare with similar skills
Data Structure Protocol next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Data Structure Protocol this skillaiskillstore/marketplace | 430 | 3 repos | ~2.5k | Automated safety check: Pass | None | |
| Bio Structural Biology Structure NavigationGPTomics/bioSkills | 1.2k | 1 repos | ~3.7k | Automated safety check: Pass | MIT | |
| Bio Pdb Structure NavigationFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2.3k | Automated safety check: Pass | None | |
| Dependency Scanningsickn33/agentic-awesome-skills | 47k | 1 repos | ~2.4k | Automated safety check: Pass | MIT | |
| Dependency Checkruvnet/ruflo | 74k | — | ~258 | Automated safety check: Pass | MIT | |
| Dependency Updatecodewhale-hq/Codewhale | 41k | — | ~142 | Automated safety check: Pass | MIT |
Similar skills
Bio Pdb Structure Navigation
FreedomIntelligence/OpenClaw-Medical-Skills
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model.
Dependency Scanning
sickn33/agentic-awesome-skills
Scan package dependencies for known vulnerabilities using Snyk, Dependabot, and OWASP Dependency-Check.
Dependency Check
ruvnet/ruflo
Scan project dependencies for known vulnerabilities and CVEs.
Dependency Update
codewhale-hq/Codewhale
Read release notes/changelogs, update a defined dependency scope, handle breaking changes, and verify.
Structured Data
thedaviddias/Front-End-Checklist
A skill your agent uses when auditing metadata, crawlability, structured data, or indexability related to Add structured data markup.
More from aiskillstore/marketplace
All 1,085 skills in this repoCode Stats
aiskillstore/marketplace
Analyze codebase with tokei (fast line counts by language) and difft (semantic AST-aware diffs).
Data Processing
aiskillstore/marketplace
Process JSON with jq and YAML/TOML with yq. An agent skill from aiskillstore/marketplace.
Doc Scanner
aiskillstore/marketplace
Scans for project documentation files (AGENTS.md, CLAUDE.md, GEMINI.md, COPILOT.md, CURSOR.md, WARP.md, and 15+ other formats) and synthesizes guidance.
File Search
aiskillstore/marketplace
Modern file and content search using fd, ripgrep (rg), and fzf.
Find Replace
aiskillstore/marketplace
Modern find-and-replace using sd (simpler than sed) and batch replacement patterns.
Investigating Codebases
aiskillstore/marketplace
Automatically activated when user asks how something works, wants to understand unfamiliar code, needs to explore a new codebase, or asks questions like "where is X implemented?", "how does Y…
Questions about Data Structure Protocol
What does Data Structure Protocol do?
Give agents persistent structural memory of a codebase — navigate dependencies, track public APIs, and understand why connections exist without re-reading the whole repo. Data Structure Protocol is an agent skill from aiskillstore/marketplace. Give agents persistent structural memory of a codebase — navigate dependencies, track public APIs, and understand why connections exist without re-reading the whole repo.
How do I install Data Structure Protocol in Claude Code?
Run `npx skills add aiskillstore/marketplace --skill data-structure-protocol -a claude-code`. Or copy the skill folder (skills/sickn33/data-structure-protocol in aiskillstore/marketplace) into .claude/skills/data-structure-protocol in your project. Claude Code loads it when a task matches its description.
How do I install Data Structure Protocol in Codex?
Run `npx skills add aiskillstore/marketplace --skill data-structure-protocol -a codex`. Or copy the skill folder (skills/sickn33/data-structure-protocol in aiskillstore/marketplace) into .agents/skills/data-structure-protocol in your project. Codex loads it when a task matches its description.
Can I use Data Structure Protocol in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aiskillstore/marketplace --skill data-structure-protocol -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/data-structure-protocol, .gemini/skills/data-structure-protocol, .github/skills/data-structure-protocol and .opencode/skills/data-structure-protocol in your project.
What does Data Structure Protocol need to run?
Going by SKILL.md and its folder, Data Structure Protocol needs the command-line tools its instructions call (python and curl). Our summary lists: Python 3.
Does Data Structure Protocol access the network?
SKILL.md names 2 domains. In commands or code: raw.githubusercontent.com; the agent is likely to contact it when it follows the instructions. As links in the text: github.com. This is read from the text; nothing was executed.
Is Data Structure Protocol safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Data Structure Protocol use?
No licence was found for Data Structure Protocol or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Data Structure Protocol use?
About 2.5k tokens (SKILL.md is roughly 9.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Data Structure Protocol?
Skills that share tags, products or a category with Data Structure Protocol: Bio Structural Biology Structure Navigation (GPTomics/bioSkills, 1.2k stars), Bio Pdb Structure Navigation (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Dependency Scanning (sickn33/agentic-awesome-skills, 47k stars) and Dependency Check (ruvnet/ruflo, 74k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Data Structure Protocol?
aiskillstore (a GitHub organization) maintains it in aiskillstore/marketplace, which has 430 GitHub stars. The repository holds 1,085 skills in this directory. The repository was last updated on October 7, 2026.
Source: aiskillstore/marketplace on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.