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PDB Database · jaechang-hits | DecimalAI

scienceby jaechang-hits

PDB Database

jaechang-hits/pdb-database

Source jaechang-hits/sciagent-skills ↗License NOASSERTION

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.

SkillScore100Maintained

Automatic

Research pack

Last verified 8/23/2026

What it changes

Passed 23 of 23 test cases with the skill, and 19 of 23 without it.

Without skill83%

With skill100%

Checks it passed that the model alone missed

Sets service to seqmotif.
Uses attribute rcsb_entity_source_organism.scientific_name.
States that RCSB PDB contains experimentally determined structures rather than predicted models.

and 1 more in the full report

4 fixed19 passed either way0 still failing0 broke

Pass-rate lift: +17 pp
Tokens: +542%
Agent turns: 0%
Response time: -43%

Model gemini-3.6-flashMeasured 8/23/2026v123 of 23 cases passed with skill

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/jaechang-hits-pdb-database/SKILL.md https://app.decimal.ai/s/jaechang-hits-pdb-database/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add jaechang-hits-pdb-database, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/jaechang-hits-pdb-database/ and pins it in .decimal/skills.lock

decimalai skills add jaechang-hits-pdb-database

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/jaechang-hits-pdb-database/SKILL.md https://app.decimal.ai/s/jaechang-hits-pdb-database/SKILL.md

Raw file: /s/jaechang-hits-pdb-database/SKILL.md ↗ · machine-readable summary at /s/jaechang-hits-pdb-database.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 4 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 4

Prompt

When searching RCSB PDB for protein entries containing a specific PROSITE amino acid motif pattern, what search service and pattern_type value must be configured in the query JSON?

What was checked, without and with the skill
Checked	Without skill	With skill
Sets service to seqmotif.	Missed	Passed
Sets pattern_type to prosite.	Passed	Passed

case-18 · gemini-3.6-flash · 8/23/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md717 linessingle file

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.

When to Use

Searching for protein or nucleic acid crystal/cryo-EM/NMR structures by keyword or property
Finding structures similar to a query sequence (MMseqs2) or 3D geometry (BioZernike)
Retrieving experimental metadata (resolution, method, organism, deposition date) for structure sets
Downloading coordinate files (PDB, mmCIF) for molecular dynamics, docking, or visualization
Building structure-based datasets for machine learning or drug discovery pipelines
Comparing protein-ligand complexes across a target family
For AlphaFold predicted structures, use alphafold-database-access instead
For protein sequence/annotation queries without structures, use uniprot-protein-database instead

Prerequisites

Python packages: requests (only requirement). Optional: biopython for parsing downloaded coordinate files.
No API key required: RCSB PDB is freely accessible.
Rate limits: No published hard limit. Polite delays of time.sleep(0.2-0.5) between requests are sufficient; implement exponential backoff on HTTP 429.

pip install requests
# Optional, for coordinate parsing:
pip install biopython

Quick Start

Track record

Benchmark

23 / 23

test cases passed, vs 19 / 23 without

Adoption

Users: 1
Times used: 16

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

jaechang-hits / sciagent-skills

skills/structural-biology-drug-discovery/pdb-database/SKILL.md

View on GitHub ↗

License BSD-3-ClauseImported 8/3/2026Version v1

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See it in action

What's inside

PDB Database

Overview

When to Use

Prerequisites

Quick Start

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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