Skill · em Dados, IA e pesquisa

pdb-database

Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/pdb-database
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
nenhum download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

2 arquivos · 23,8 KB · só texto, nenhum script

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/pdb-database/.

d=".claude/skills/pdb-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pdb-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/pdb-database/.

d="$HOME/.claude/skills/pdb-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pdb-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/pdb-database/.

d=".agents/skills/pdb-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pdb-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/pdb-database/.

d="$HOME/.agents/skills/pdb-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pdb-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/pdb-database/.

d=".agents/skills/pdb-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pdb-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/pdb-database/.

d="$HOME/.gemini/antigravity-cli/skills/pdb-database"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pdb-database"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/api_reference.md" "$u/references/api_reference.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.pdb-database

Prévia do SKILL.md

---
name: pdb-database
description: "Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery."
---

# PDB Database

## Overview

RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules. Search for structures, retrieve coordinates and metadata, perform sequence and structure similarity searches across 200,000+ experimentally determined structures and computed models.

## When to Use This Skill

This skill should be used when:
- Searching for protein or nucleic acid 3D structures by text, sequence, or structural similarity
- Downloading coordinate files in PDB, mmCIF, or BinaryCIF formats
- Retrieving structural metadata, experimental methods, or quality metrics
- Performing batch operations across multiple structures
- Integrating PDB data into computational workflows for drug discovery, protein engineering, or structural biology research

## Core Capabilities

### 1. Searching for Structures

Find PDB entries using various search criteria:

**Text Search:** Search by protein name, keywords, or descriptions
```python
from rcsbapi.search import TextQuery
query = TextQuery("hemoglobin")
results = list(query())
print(f"Found {len(results)} structures")
```

**Attribute Search:** Query specific properties (organism, resolution, method, etc.)
```python
from rcsbapi.search import AttributeQuery
from rcsbapi.search.attrs import rcsb_entity_source_organism

# Find human protein structures
…

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