pdbe-api

Enables querying the PDBe API from Coot for accessing protein structure metadata and validation data efficiently.

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48/100

Security score

The pdbe-api skill was audited on Jun 12, 2026 and we found 38 security issues across 2 threat categories, including 1 high-severity. Review the findings below before installing.

Categories Tested

Security Issues

high line 726

Hex-encoded characters

SourceSKILL.md

726	if result.startswith(b'\x1f\x8b'): # gzip magic bytes

low line 24

External URL reference

SourceSKILL.md

24	result = coot.coot_get_url_as_string_py("https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/4wa9")

low line 29

External URL reference

SourceSKILL.md

29	compressed = coot.coot_get_url_as_string_py("https://files.rcsb.org/download/4wa9.cif.gz")

low line 37

External URL reference

SourceSKILL.md

37	Base URL: `https://www.ebi.ac.uk/pdbe/api/`

low line 39

External URL reference

SourceSKILL.md

39	Documentation: https://www.ebi.ac.uk/pdbe/api/doc/

low line 42

External URL reference

SourceSKILL.md

42	Base URL: `https://www.ebi.ac.uk/pdbe/graph-api/`

low line 44

External URL reference

SourceSKILL.md

44	Documentation: https://pdbe.org/graph-api

low line 47

External URL reference

SourceSKILL.md

47	Base URL: `https://www.ebi.ac.uk/pdbe/search/pdb/select?`

low line 49

External URL reference

SourceSKILL.md

49	Documentation: https://www.ebi.ac.uk/pdbe/api/doc/search.html

low line 61

External URL reference

SourceSKILL.md

61	url = f"https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{pdb_id}"

low line 95

External URL reference

SourceSKILL.md

95	url = f"https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/{pdb_id}"

low line 124

External URL reference

SourceSKILL.md

124	url = f"https://www.ebi.ac.uk/pdbe/api/pdb/compound/summary/{comp_id}"

low line 153

External URL reference

SourceSKILL.md

153	url = f"https://files.rcsb.org/download/{pdb_id}.cif.gz"

low line 178

External URL reference

SourceSKILL.md

178	url = f"https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/{pdb_id}"

low line 201

External URL reference

SourceSKILL.md

201	url = f"https://www.ebi.ac.uk/pdbe/api/pdb/entry/status/{pdb_id}"

low line 224

External URL reference

SourceSKILL.md

224	url = f"https://www.ebi.ac.uk/pdbe/api/pdb/entry/ligand_monomers/{pdb_id}"

low line 248

External URL reference

SourceSKILL.md

248	url = f"https://www.ebi.ac.uk/pdbe/api/pdb/entry/assembly/{pdb_id}"

low line 324

External URL reference

SourceSKILL.md

324	url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select?q={query}&wt=json&rows=10&fl=pdb_id,title,resolution"

low line 404

External URL reference

SourceSKILL.md

404	url = "https://www.ebi.ac.uk/pdbe/search/pdb/select?q=release_year:2024%20AND%20experimental_method:\"X-ray%20diffraction\"%20AND%20resolution:[*%20TO%201.5]&wt=json&rows=5&fl=pdb_id,title,resolution"

low line 424

External URL reference

SourceSKILL.md

424	url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select?q={query}&wt=json&rows=10&fl=pdb_id,title,resolution"

low line 430

External URL reference

SourceSKILL.md

430	url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select?q={query}&wt=json&rows=10&fl=pdb_id,title,em_resolution"

low line 436

External URL reference

SourceSKILL.md

436	url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select?q={query}&wt=json&rows=10&fl=pdb_id,title"

low line 443

External URL reference

SourceSKILL.md

443	url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select?q={query}&wt=json&rows=100&fl=pdb_id,organism_scientific_name,title"

low line 450

External URL reference

SourceSKILL.md

450	url = "https://www.ebi.ac.uk/pdbe/search/pdb/select?q=:&wt=json&rows=1&fl=*"

low line 493

External URL reference

SourceSKILL.md

493	url = f"https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{pdb_id}"

low line 535

External URL reference

SourceSKILL.md

535	url = f"https://www.ebi.ac.uk/pdbe/api/pdb/compound/summary/{comp_id}"

low line 567

External URL reference

SourceSKILL.md

567	url = f"https://files.rcsb.org/download/{pdb_id}.cif.gz"

low line 609

External URL reference

SourceSKILL.md

609	url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select?q={query}&wt=json&rows=100&fl=pdb_id,organism_scientific_name"

low line 649

External URL reference

SourceSKILL.md

649	url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select?q={query}&wt=json&rows=50&fl=pdb_id,title,resolution,organism_scientific_name"

low line 710

External URL reference

SourceSKILL.md

710	data = safe_pdbe_query("https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/4wa9")

low line 771

External URL reference

SourceSKILL.md

771	url = f"https://www.ebi.ac.uk/pdbe/search/pdb/select?q={encoded}&wt=json"

low line 783

External URL reference

SourceSKILL.md

783	data = safe_pdbe_query(f"https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{pdb_id}")

low line 801

External URL reference

SourceSKILL.md

801	\| Download coordinates \| `https://files.rcsb.org/download/{pdb_id}.cif.gz` \|

low line 850

External URL reference

SourceSKILL.md

850	data = safe_pdbe_query(f"https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{pdb_id}")

low line 880

External URL reference

SourceSKILL.md

880	- PDBe API Documentation: https://www.ebi.ac.uk/pdbe/api/doc/

low line 881

External URL reference

SourceSKILL.md

881	- Aggregated API: https://pdbe.org/graph-api

low line 882

External URL reference

SourceSKILL.md

882	- Search API: https://www.ebi.ac.uk/pdbe/api/doc/search.html

low line 885

External URL reference

SourceSKILL.md

885	- RCSB Downloads: https://files.rcsb.org/download/

Scanned on Jun 12, 2026

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Categoryeducation research

UpdatedJune 15, 2026

openclaw api researcher data-scientist education research data analytics

pemsley/coot