# 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.

## Install

```bash
npx skillstore add davila7/pdb-database
```

## Metadata

- Status: approved
- Slug: davila7-pdb-database
- Skillstore revision: r2
- Version status: missing
- Tree hash: 26ce51b5a7f27bee6f247bd5627454f5f29ccb09d1496224e1604af45f77e99d
- Author: davila7
- GitHub username: davila7
- License: MIT
- Repository: https://github.com/davila7/claude-code-templates/tree/main/cli-tool/components/skills/scientific/pdb-database
- Ref: c43861a65bb95efcae259cd161c9d6f4dc7eec6f
- Supported tools: Claude, Codex, Claude Code
- Audit status: complete
- Agent install advisory: allowed
- Manual install advisory: allowed
- Artifact signature: available
- Audit attestation: unavailable
- Human verification: not\_verified
- Risk factors: external\_commands, network, filesystem
- Quality score: 74
- Public page: https://skillstore.pages.dev/skills/davila7-pdb-database
- Manifest: https://skillstore.pages.dev/api/skills/davila7-pdb-database/manifest

## Capabilities

- Searches RCSB PDB by text, attributes, sequence similarity, or structural similarity.
- Combines search criteria with logical operators.
- Retrieves entry, polymer entity, assembly, and experimental metadata.
- Downloads PDB, mmCIF, biological assembly, and FASTA data.
- Provides examples for batch retrieval, retries, parsing, and quality filtering.

## Use Cases

- Screen Drug Targets: Find high-quality target structures, inspect ligands, and retrieve coordinates for downstream modeling.
- Compare Protein Variants: Locate homologous or mutant structures and collect metadata for sequence-structure comparisons.
- Build Teaching Datasets: Select representative structures and download files for molecular visualization exercises.

## Prompt Templates

### Find Structures

```
Find RCSB PDB structures for [protein name]. Return PDB IDs, titles, organisms, methods, and resolutions.
```

### Filter by Quality

```
Find [organism] structures for [target] with resolution below [value] angstroms. Explain the filters and summarize the strongest matches.
```

### Search by Sequence

```
Search RCSB PDB for structures similar to [sequence] using identity [value] and E-value [value]. Summarize candidate coverage and experimental quality.
```

### Design a Batch Workflow

```
Design a rate-limited workflow for [PDB IDs]. Retrieve selected metadata, download mmCIF files to [directory], handle failures, and report incomplete records.
```

## Limitations

- Requires network access to RCSB services for live searches and retrieval.
- Requires external Python packages for the documented client and parsing examples.
- Does not validate scientific conclusions or assess biological significance.
- API availability, schemas, rate limits, and package interfaces may change.

## Best Practices

- Use mmCIF for modern workflows and large structures.
- Validate PDB identifiers and review metadata before downstream analysis.
- Respect RCSB rate limits and cache repeated query results.

## Anti Patterns

- Do not treat the first search result as scientifically definitive.
- Do not compare structures without checking assemblies, methods, and resolution.
- Do not run large batches without delays, retries, and failure reporting.

## Security Audit

- Audited at: 2026-07-23T14:51:06.671\+00:00
- 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.

## Stats

- Views: 224
- Downloads: 9
- Favorites: 0
- Popularity score: 0