Explore RCSB Protein Structures
Finding relevant macromolecular structures and metadata can require several RCSB interfaces. This skill guides focused searches, retrieval, downloads, and batch workflows.
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Review the Skillstore skill "pdb-database" from https://skillstore.io/skills/davila7-pdb-database.md and its manifest at https://skillstore.io/api/skills/davila7-pdb-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Using "pdb-database". Find human hemoglobin structures determined by X-ray diffraction at better than 2.0 angstrom resolution.
Expected outcome:
Using "pdb-database". Retrieve entry metadata for 4HHB and explain the most useful quality fields.
Expected outcome:
A concise record covering title, method, resolution, deposition date, atom count, and guidance for interpreting available quality indicators.
Using "pdb-database". Plan downloads for 4HHB, 1MBN, and 1GZX in mmCIF format.
Expected outcome:
A three-entry download plan with official RCSB sources, destination filenames, rate-limit handling, and a clear failure summary.
All 81 static findings are false positives caused by documentation examples, Markdown formatting, or expected access to official RCSB services. No prompt injection, concealed execution, data exfiltration, or unrelated system reconnaissance was found.
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https://skillstore.io/skills/davila7-pdb-database/audits/10?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report[](https://skillstore.io/skills/davila7-pdb-database?utm_source=security_passport_badge)<a href="https://skillstore.io/skills/davila7-pdb-database?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/davila7-pdb-database/security.svg" alt="Skillstore security assessment" loading="lazy"></a><iframe src="https://skillstore.io/embed/skills/davila7-pdb-database.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>davila7. (2026). pdb-database security audit report (audit version 10) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-pdb-database/audits/10@techreport{davila7-davila7-pdb-database-2026,
author = {davila7},
title = {pdb-database security audit report (audit version 10)},
institution = {Skillstore},
year = {2026},
number = {10},
url = {https://skillstore.io/skills/davila7-pdb-database/audits/10},
note = {Author version unspecified}
}cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "pdb-database security audit report (audit version 10)"
version: "unspecified"
type: report
authors:
- name: "davila7"
date-released: "2026-07-23"
url: "https://skillstore.io/skills/davila7-pdb-database/audits/10"
identifiers:
- type: other
value: "skillstore:davila7-pdb-database:audit:10"
description: "Skillstore immutable audit report identifier"
Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
davila7-pdb-database
2026-08-21
k-dense-ai-pdb-database
2026-08-21
Find high-quality target structures, inspect ligands, and retrieve coordinates for downstream modeling.
Locate homologous or mutant structures and collect metadata for sequence-structure comparisons.
Select representative structures and download files for molecular visualization exercises.
Find RCSB PDB structures for [protein name]. Return PDB IDs, titles, organisms, methods, and resolutions.
Find [organism] structures for [target] with resolution below [value] angstroms. Explain the filters and summarize the strongest matches.
Search RCSB PDB for structures similar to [sequence] using identity [value] and E-value [value]. Summarize candidate coverage and experimental quality.
Design a rate-limited workflow for [PDB IDs]. Retrieve selected metadata, download mmCIF files to [directory], handle failures, and report incomplete records.
Author
davila7License
MIT
Skillstore revision
r2
Version notice
The author did not declare a version.
Ref
c43861a65bb95efcae259cd161c9d6f4dc7eec6f
Maintenance freshness
7/24/2026
Usage
7 downloads · 224 views
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