Evidence Insight

pdb-database

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.

86100Total Score

Core Capability

84 / 100

Functional Suitability

11 / 12

Reliability

9 / 12

Performance & Context

7 / 8

Agent Usability

14 / 16

Human Usability

8 / 8

Security

10 / 12

Maintainability

9 / 12

Agent-Specific

16 / 20

Medical Task

20 / 20 Passed

92Find protein/nucleic acid 3D structures by keywords, organism, experimental method, or resolution

4/4

88Identify related structures via sequence similarity (e.g., homolog search for modeling)

4/4

86Text and attribute-based search over RCSB PDB entries

4/4

86Sequence similarity search with configurable thresholds (e-value, identity)

4/4

86End-to-end case for Text and attribute-based search over RCSB PDB entries

4/4

Veto GatesRequired pass for any deployment consideration

Skill Veto✓ All 4 gates passed

✓

Operational Stability

System remains stable across varied inputs and edge cases

PASS

✓

Structural Consistency

Output structure conforms to expected skill contract format

PASS

✓

Result Determinism

Equivalent inputs produce semantically equivalent outputs

PASS

✓

System Security

No prompt injection, data leakage, or unsafe tool use detected

PASS

Research Veto✅ PASS — Applicable

Dimension	Result	Detail
Scientific Integrity	PASS	The legacy audit did not indicate that retrieval outputs were presented as unsupported findings.
Practice Boundaries	PASS	Practice boundaries held because the package remained focused on source handling, lookup, or structured evidence use.
Methodological Ground	PASS	The older review treated the package logic as methodologically aligned with its stated workflow.
Code Usability	N/A	The package is evaluated primarily as a structured deliverable rather than an executable scientific code workflow.

Core Capability84 / 100 — 8 Categories

Functional Suitability

Functional suitability was softened by the legacy issue 'Improve stress-case output rigor'. Stress and boundary scenarios show weaker consistency

11 / 12

92%

Reliability

The archived deduction in reliability traces back to: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency

9 / 12

75%

Performance & Context

A modest deduction remained in performance context for pdb-database in the archived review.

7 / 8

88%

Agent Usability

The legacy audit deducted points for pdb-database in agent usability.

14 / 16

88%

Human Usability

No point loss was recorded for human usability in the legacy audit.

8 / 8

100%

Security

The archived evaluation left some headroom for pdb-database under security.

10 / 12

83%

Maintainability

A modest deduction remained in maintainability for pdb-database in the archived review.

9 / 12

75%

Agent-Specific

The archived deduction in agent specific traces back to: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency

16 / 20

80%

Core Capability Total84 / 100

Medical TaskExecution Average: 87.6 / 100 — Assertions: 20/20 Passed

Canonical

Find protein/nucleic acid 3D structures by keywords, organism, experimental method, or resolution

4/4 ✓

Variant A

Identify related structures via sequence similarity (e.g., homolog search for modeling)

4/4 ✓

Edge

Text and attribute-based search over RCSB PDB entries

4/4 ✓

Variant B

Sequence similarity search with configurable thresholds (e-value, identity)

4/4 ✓

Stress

End-to-end case for Text and attribute-based search over RCSB PDB entries

4/4 ✓

Canonical✅ Pass

Find protein/nucleic acid 3D structures by keywords, organism, experimental method, or resolution

The archived run for Find protein/nucleic acid 3D structures by keywords, organism,... remained guidance-driven rather than command-driven.

Basic 36/40|Specialized 56/60|Total 92/100

✅A1The pdb-database output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Variant A✅ Pass

Identify related structures via sequence similarity (e.g., homolog search for modeling)

The archived run for Identify related structures via sequence similarity (e.g., homolog... remained guidance-driven rather than command-driven.

Basic 34/40|Specialized 54/60|Total 88/100

✅A1The pdb-database output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Edge✅ Pass

Text and attribute-based search over RCSB PDB entries

Text and attribute-based search over RCSB PDB entries was evaluated as a bounded documentation path, not as a runnable script workflow.

Basic 33/40|Specialized 53/60|Total 86/100

✅A1The pdb-database output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Variant B✅ Pass

Sequence similarity search with configurable thresholds (e-value, identity)

The archived run for Sequence similarity search with configurable thresholds (e-value,... remained guidance-driven rather than command-driven.

Basic 32/40|Specialized 54/60|Total 86/100

✅A1The pdb-database output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Stress✅ Pass

End-to-end case for Text and attribute-based search over RCSB PDB entries

This stress case stayed inside the documented workflow and remained instruction-led.

Basic 29/40|Specialized 57/60|Total 86/100

✅A1The pdb-database output structure matches the documented deliverable

✅A2The instruction path remains actionable for the documented case

✅A3The output stays fully within the documented skill boundary

✅A4The response quality is acceptable for the documented path

Pass rate: 4 / 4

Medical Task Total87.6 / 100

Key Strengths

Primary routing is Evidence Insight with execution mode A
Static quality score is 84/100 and dynamic average is 79.6/100
Assertions and command execution outcomes are recorded per input for human review
Execution verification summary: No script verification was applicable