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.

1.69x

Quality

77%

Does it follow best practices?

Impact

83%

1.69x

Average score across 3 eval scenarios

Securityby

Passed

No known issues

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/pdb-database/SKILL.md

Evaluation results

84%

64%

Drug Target Structure Discovery

Combined attribute search with correct package

Criteria

Without context

With context

Correct package import

100%

No deprecated package

100%

uv installation

TextQuery usage

100%

AttributeQuery usage

100%

Attribute operator specificity

100%

Bitwise combination

100%

Attribute module import

Resolution filter

50%

100%

Results iterated correctly

100%

Output file produced

100%

rcsb-api package name

100%

80%

24%

Protein Structure Analysis Pipeline

Structure download and BioPython parsing

Criteria

Without context

With context

rcsbapi.data import

75%

Schema constant used

PDB download URL pattern

100%

mmCIF or PDB format

100%

BioPython parser

100%

Structure hierarchy traversal

100%

Resolution field access

62%

87%

Experimental method field

100%

Correct package import path

100%

No deprecated package

100%

Output file produced

100%

uv installation

87%

14%

Homolog Structure Dataset Builder

Sequence similarity search with batch rate limiting

Criteria

Without context

With context

SequenceQuery import

evalue_cutoff parameter

77%

100%

identity_cutoff parameter

77%

100%

Exponential backoff logic

100%

429 handling

100%

Delay between batch requests

100%

Search-then-fetch pattern

100%

rcsbapi.data fetch

37%

No deprecated package

100%

uv installation

100%

Results limited or chunked

100%

Output file produced

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: 71add64

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Drug Target Structure Discovery Protein Structure Analysis Pipeline Homolog Structure Dataset Builder

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