pdb-database SKILL.md skillA
pdb-database from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/pdb-database@git:20260522.6a6fd41Pins git:20260522.6a6fd41 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/structural-biology-drug-discovery/pdb-database/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260522.6a6fd41, committed May 22, 2026
- First version recorded
- Feb 18, 2026
- Size
- 31,067 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# PDB Database
> **Why no SDK?** The `rcsb-api` Python SDK is convenient sugar over three public, no-auth REST endpoints (`search.rcsb.org`, `data.rcsb.org`, `files.rcsb.org`). When the SDK is unavailable, every operation can be reproduced with plain `requests` and a small JSON payload. This SKILL.md uses the REST path throughout so the code runs in any environment with `requests` installed.
## Overview
RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules with 200,000+ experimentally determined structures. Programmatic access is via three free, no-auth endpoints:
| API | Base URL | Method | Purpose |
|---|---|---|---|
| **Search** | `https://search.rcsb.org/rcsbsearch/v2/query` | `POST` JSON | Find PDB IDs by text, attribute filters, sequence, or 3D similarity |
| **Data** | `https://data.rcsb.org/graphql` | `POST` GraphQL | Retrieve structured metadata (entries, polymer entities, assemblies, ligands) |
| **Files** | `https://files.rcsb.org/download/{id}.{format}` | `GET` | Download coordinate files (mmCIF, PDB, FASTA) |
Use this skill for programmatic structural biology queries, drug target analysis, and protein family comparisons.
…Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/pdb-database@sha256:ea38c4f96a47aac9The line at the top of this page pins the label git:20260522.6a6fd41, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_ylhepqd2hvfqwxy3)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Feb 18, 2026 and May 22, 2026, about one every 31 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260522.6a6fd41 latest | 2026-05-22 | 6a6fd41 | 31,067 B | A | view · diff |
| git:20260428.81ea2d2 | 2026-04-28 | 81ea2d2 | 21,742 B | A | view · diff |
| git:20260409.a3b01d0 | 2026-04-09 | a3b01d0 | 21,818 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 21,856 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (31067 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ylhepqd2hvfqwxy3 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/pdb-database GET https://markdownregistry.com/api/v1/blob/ea38c4f96a47aac96f36a5c85f1918a474da46ae504dd04198954a21391a3183
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.