Claude Code, Skill
Drug Discovery Agent Skills
Agent Skills for small-molecule and protein therapeutics: target validation and human genetics, bioactivity and chemical space, generative design and retrosynthesis, docking, free energy and dynamics, ADMET and PK translation, protein, antibody, degrader and oligonucleotide desig
Compatibility: Not stated.
Grade D
Two or more Medium findings, or a High finding. Only try it in a sandbox.
Not a guarantee. A hygiene check of the source at the commit shown, not a security audit.
NETWORK_HOST_FROM_INPUT OBFUSCATION_ENCODED_BLOB
Why this grade
- NETWORK_HOST_FROM_INPUT Medium
A file takes a URL or endpoint as input and has no fixed host list.
skills/adaptyv/SKILL.md, line 30
curl https://foundry-api-public.adaptyvbio.com/api/v1/targets?limit=3 \ - OBFUSCATION_ENCODED_BLOB Medium
Contains a long base64 shaped string in a file that should be readable.
uv.lock, line 1
version = 1
Any High, or two or more Medium findings, give D. One Medium gives C. Low findings or a security Note give B. Each code names a finding behind the letter.
If you think this grade is wrong, email [email protected] with the entry link and your evidence. We aim to acknowledge within two working days and decide within seven. If we confirm an error, we aim to correct it within 24 hours of confirming it. These are aims, not guarantees.
Grades are a hygiene check of the source at the commit shown, on the date checked, not a security audit or a guarantee. The free directory grades are automated. Before release, a PlugVet engineer reviews every paid report and any grade we hold back, including all F grades, against the source code and the evidence we quote.
What was checked
Plain notes from the hygiene checks.
Permissions
Note
requests shell access. The manifest names this permission.
PERMISSION_SHELL_DECLARED
skills/autodock-vina/scripts/dock_batch.py, line 68
result = subprocess.run([vina, "--version"], capture_output=True, text=True, timeout=30)
skills/autodock-vina/scripts/dock_batch.py, line 85
result = subprocess.run(command, capture_output=True, text=True, timeout=timeout)
docs/security-report.json, line 1776
"description": "dock_batch.py locates and executes external executables (vina, mk_prepare_ligand.py, mk_prepare_receptor.py, mk_export.py, scrub.py, obabel) via shutil.which() and
Show more
docs/security-report.json, line 1779
"snippet": "def which(name: str) -> str | None:\n return shutil.which(name)\n...\nresult = subprocess.run(command, capture_output=True, text=True, timeout=timeout)",
docs/security-report.md, line 202
> dock_batch.py locates and executes external executables (vina, mk_prepare_ligand.py, mk_prepare_receptor.py, mk_export.py, scrub.py, obabel) via shutil.which() and subprocess.run
Install and update
Pass
No install-time script found, and dependencies are pinned or absent.
Network
Serious
accepts a host from input, with no fixed list in this file.
NETWORK_HOST_FROM_INPUT
skills/adaptyv/SKILL.md, line 30
curl https://foundry-api-public.adaptyvbio.com/api/v1/targets?limit=3 \
skills/chembl/scripts/_common.py, line 104
with urllib.request.urlopen(request, timeout=timeout) as response:
skills/chemical-space/scripts/_common.py, line 88
with urllib.request.urlopen(request, timeout=timeout) as response:
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skills/clinicaltrials/scripts/_common.py, line 87
with urllib.request.urlopen(request, timeout=timeout) as response:
skills/depmap/SKILL.md, line 87
response = requests.get(url, stream=True)
skills/glycoengineering/SKILL.md, line 262
response = requests.get(url, headers={"Accept": "application/json"})
skills/glycoengineering/references/glycan_databases.md, line 17
response = requests.get(url, headers={"Accept": "application/json"})
skills/glycoengineering/references/glycan_databases.md, line 33
response = requests.get(f"{base_url}/proteins/uniprot/{uniprot_id}")
skills/patent-landscape/scripts/surechembl_bulk.py, line 187
print(f"curl -O {row['url']}", file=sys.stderr)
Secrets
Concern
reads a credential or environment file.
SECRETS_ENV_READ SECRETS_PATH_DOTENV
scan_pr_skills.py, line 264
if not os.getenv("SKILL_SCANNER_LLM_API_KEY"):
scan_skills.py, line 129
# collection pattern (`config`, `token`, `private`, `.env`) and a *different*
scan_skills.py, line 152
llm_key = os.getenv("SKILL_SCANNER_LLM_API_KEY")
Show more
skills/openfda/scripts/_common.py, line 68
key = os.environ.get("OPENFDA_API_KEY", "").strip()
skills/patent-landscape/scripts/_common.py, line 75
key = os.environ.get("PATENTSVIEW_API_KEY", "").strip()
.env.example, line 3
# Copy to `.env` and fill in only the values you need - every variable here is
.env.example, line 7
# cp .env.example .env
.env.example, line 9
# `.env` is gitignored. Never commit real keys. Scripts that read this file use
.gitignore, line 10
# Secrets
CONTRIBUTING.md, line 274
# needs SKILL_SCANNER_LLM_API_KEY (see .env.example)
docs/security-report.json, line 1473
"llm_overall_assessment": "The `adaptyv` skill is a documentation-only skill describing the Adaptyv Bio Foundry REST API and Python SDK. It contains no script files, no obfuscated
docs/security-report.json, line 1477
"Broad .env credential file access",
Agent instructions
Pass
No instruction to ignore earlier instructions or to hide a step.
Obfuscation
Concern
contains an encoded blob in a file that should be readable.
OBFUSCATION_ENCODED_BLOB
uv.lock, line 1
version = 1
docs/security-report.json, line 1
{
skills/diffdock/references/workflows_examples.md, line 79
--protein_sequence "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNG
Show more
skills/diffdock/scripts/prepare_batch_csv.py, line 175
'MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLA
skills/esm/references/biohub-platform.md, line 49
sequence = "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIR
skills/glycoengineering/SKILL.md, line 90
fc_sequence = "APELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTP
skills/diffdock/assets/batch_template.csv, line 3
example_2,,COc1ccc(C#N)cc1,MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIM
Licence
Pass
A licence file is present (LICENSE.md).
Maintainer activity
Pass
The latest commit is within the last 365 days.
Note
Hygiene check of commit c1037e410962. requests shell access. The manifest names this permission. accepts a host from input, with no fixed list in this file. reads a credential or environment file. contains an encoded blob in a file that should be readable.
Date and source
Date checked:
github.com
Commit graded: c1037e4109624ebcd4c073b68ce63f969323592c
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