Public record
Software health reportschema 0.12.0 · metrics 2.10.0 · 2026-07-17 18:15 UTC

pdbeurope / pdbe-mcp-servers

PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.

PythonApache-2.0★ 36 stars⑂ 1 forksince Jun 2025View on GitHub ↗
KindMCP serverLibraryNetwork serviceCommand-line toolhow this is determined
#ai-integration#api-server#bioinformatics#knowledge-graph#llm-tools#mcp#pdbe#protein-structures#python#structural-biology

pdbeurope/pdbe-mcp-servers holds a health index of 78 out of 100, placing it in the Good band. It scores highest on Vitality (81/100) and lowest on Community & Adoption (46/100). It was last updated today. A single contributor accounts for most of its recent work.

78
overall / 100
Good

Software health index

Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean, calibrated against the distribution of the public record so bands carry percentile meaning; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At Risk ceiling of 34.

78
Exceptional93-100The record's top tier (≈ top 5%); essentially all checked criteria met
Excellent80-92Strong across the board; minor gaps
Good65-79Healthy; gaps are limited and manageable
Moderate50-64Acceptable with notable gaps; review recommended
Weak35-49Material weaknesses across several areas
At Risk20-34Significant weaknesses; adoption warrants caution
Critical1-19Severe problems (abandoned, single-maintainer, no hygiene)
VitalityCommunity &AdoptionSustainability &GovernanceEngineeringQualitySecurityAI Readiness

Score profile

Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.

The weighted overall 67 is calibrated to 78 on the published index scale (record calibration 2026-08-02).

Ownership

PDBe EMBL-EBIOrganization
86 followers48 public repossince Sep 2014

This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPIpdbe-mcp-server1.1.53,297162 days agoautomationfetchhttpllmmcpstatelessstreamableweb

Metrics by category

Vitality

Is the project alive — is code being written and are releases shipping?

81Excellent · 21% of overall

Development activity

69Good
How it's scored
36/36Push recency — last push 0 days ago
10.4/36Commit cadence — 15/52 weeks with commits
12.6/18Commit volume — 24 commits in the last year
10/10OpenSSF Scorecard: Maintained — 14 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year24
human_commit_share—
days_since_last_push0
active_weeks_last_year15

Release discipline

100Exceptional
How it's scored
27/27Ships releases — 17 releases published
36/36Release recency — latest release 2 days ago
27/27Release cadence — a release every ~8.6 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count17
latest_release_tagv1.1.6
releases_from_tagsno
days_since_latest_release2
mean_days_between_releases8.6
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.

Community & Adoption

Does the project have users, downloads, attention, and a welcoming setup for contributors?

46Weak · 17% of overall

Popularity & adoption

25At Risk
How it's scored
25/60Stars — 36 stars
0/25Forks — 1 forks
0/15Watchers — 0 watchers
Inputs used
forks1
stars36
watchers0
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

70Good
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (Apache-2.0)
18/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges—
has_contributingyes
has_issue_templateno
has_code_of_conductno
readme_badge_services—
has_pull_request_templateno

Sustainability & Governance

Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?

65Good · 23% of overall

Maintainer resilience (bus factor)

18Critical
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
0.7/22.5Commit distribution — top contributor authored 97% of commits
2.7/13.5Contributor breadth — 2 contributors
6/10OpenSSF Scorecard: Contributors — project has 2 contributing companies or organizations -- score normalized to 6
Inputs used
bus_factor1
contributors_sampled2
top_contributor_share0.968

Issue & PR responsiveness

73Good
How it's scored
42/42Issue resolution — 100% of issues closed
21.7/30PR acceptance — 26/36 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
0/15OpenSSF Scorecard: Code-Review — Found 0/27 approved changesets -- score normalized to 0
Inputs used
merged_prs26
open_issues0
closed_issues2
prs_merged_7d—
prs_decided_7d—
prs_merged_30d—
prs_decided_30d—
issue_closed_ratio1
closed_unmerged_prs10
first_time_authors_30d—
first_time_prs_merged_30d—
first_time_prs_decided_30d—
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

85Excellent
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain — verified-domain status not read for this organization
13.9/25Owner reach — 86 followers of PDBeurope
24.3/25Track record — 48 public repos, account ~11 yr old
Inputs used
followers86
owner_typeOrganization
is_verified—
owner_loginPDBeurope
public_repos48
account_age_days4,321
Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
35/35Publish recency — latest publish 2 days ago
20/20Version history — 16 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagespdbe-mcp-server
ecosystemspypi
any_deprecatedno
min_days_since_publish2

Engineering Quality

Are baseline engineering and documentation practices in place?

78Good · 19% of overall

Engineering practices

90Excellent
How it's scored
24/24CI workflows — 1 workflow(s)
24/24Tests present
16/16Linter config — ruff.toml
9.6/9.6Pre-commit hooks
0/6.4.editorconfig
16/20OpenSSF Scorecard: CI-Tests — 23 out of 26 merged PRs checked by a CI test -- score normalized to 8
Inputs used
has_ciyes
has_testsyes
has_editorconfigno
has_linter_configyes
has_precommit_configyes

Documentation

60Moderate
How it's scored
30/30README
0/25Documentation directory
0/15Documentation / homepage site
10/10Repository description
10/10Topics — 10 topics
10/10Wiki
Inputs used
topicsai-integration, api-server, bioinformatics, knowledge-graph, llm-tools, mcp, pdbe, protein-structures, python, structural-biology
has_wikiyes
homepage—
docs_site—
has_readmeyes
has_docs_dirno
has_descriptionyes

Security

Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?

65Good · 16% of overall

Security posture

65Good
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — no data
2/2.5CI-Tests — 23 out of 26 merged PRs checked by a CI test -- score normalized to 8
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0/7.5Code-Review — Found 0/27 approved changesets -- score normalized to 0
1.5/2.5Contributors — project has 2 contributing companies or organizations -- score normalized to 6
10/10Dangerous-Workflow — no dangerous workflow patterns detected
7.5/7.5Dependency-Update-Tool — update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5License — license file detected
7.5/7.5Maintained — 14 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10
5/5Packaging — packaging workflow detected
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
2/5SAST — SAST tool is not run on all commits -- score normalized to 4
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — no data
7.5/7.5Token-Permissions — GitHub workflow tokens follow principle of least privilege
5.2/7.5Vulnerabilities — 3 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate6.5
Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.

AI Readiness

How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.

51Moderate · 4% of overall

Agent context & guidance

1Critical
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
0/40Legible commit history — no data
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share—
agent_instruction_files—
agent_instruction_max_bytes—
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.

Verify loop (build / test / typecheck)

88Excellent
How it's scored
18/18One-command bootstrap — Makefile
22/22Automated tests
11/11Lint / format config — ruff.toml
11/11Static type checking — pdbe_mcp_server/py.typed
10/10Reproducible environment — lockfile
0/10Demonstrated agent practice — no data
0/8Automated maintenance — no data
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfilesuv.lock
has_dockerfileno
typed_languageno
bootstrap_filesMakefile
has_devcontainerno
has_linter_configyes
typecheck_configspdbe_mcp_server/py.typed
agent_commit_share—
toolchain_manifests—
dependency_bot_commit_share—
Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance. Remaining weights renormalized.

Code legibility for models

82Excellent
How it's scored
27/45Type-checkable code — Python with type-check config (pdbe_mcp_server/py.typed)
55/55Manageable file sizes — 0/15 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes28,927
source_files_sampled15
oversized_source_files0

Machine-readable interfaces

20At Risk
How it's scored
0/40API schema (OpenAPI/GraphQL/proto)
20/20MCP server
0/40Runnable examples
Inputs used
example_dirs—
has_mcp_signalyes
api_schema_files—
interfaces_expected_ofnetwork-service

Key facts

36GitHub stars
2contributors
24commits, last 12 months
0days since last push
17releases
1bus factor
0open issues
PyPIpackage ecosystems

More detail

OpenSSF Scorecard 6.5 / 10
6.5aggregate

Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).Scorecard v5.5.0 · 2026-07-17 18:15 UTC

10Binary-Artifactsno binaries found in the repo
n/aBranch-Protectioninternal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md
8CI-Tests23 out of 26 merged PRs checked by a CI test -- score normalized to 8
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 0/27 approved changesets -- score normalized to 0
6Contributorsproject has 2 contributing companies or organizations -- score normalized to 6
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained14 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10
10Packagingpackaging workflow detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
4SASTSAST tool is not run on all commits -- score normalized to 4
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
10Token-PermissionsGitHub workflow tokens follow principle of least privilege
7Vulnerabilities3 existing vulnerabilities detected
Direct dependencies 10
RegistryPackageVersion constraintManifest
PyPIanyio>=4.5pyproject.toml
PyPIclick>=8.1.0pyproject.toml
PyPIhttpx>=0.27pyproject.toml
PyPImcp>=1.23.0pyproject.toml
PyPIneo4j>=5.0pyproject.toml
PyPIomegaconf>=2.3.0pyproject.toml
PyPIpython-toon>=0.1.3pyproject.toml
PyPIrequests>=2.33.0pyproject.toml
PyPIstarlette>=1.0.1pyproject.toml
PyPIuvicorn—pyproject.toml
All dependencies 79

Full resolved dependency set from the GitHub dependency graph: 10 direct and 69 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPIanyio4.9.0direct
PyPIclick8.2.1direct
PyPIhttpx0.28.1direct
PyPImcp1.27.2direct
PyPIneo4j6.1.0direct
PyPIomegaconf2.3.0direct
PyPIpython-toon0.1.3direct
PyPIrequests2.34.2direct
PyPIstarlette1.3.1direct
PyPIuvicorn0.34.3direct
PyPIannotated-types0.7.0indirect
PyPIantlr4-python3-runtime4.9.3indirect
PyPIattrs26.1.0indirect
PyPIbackports-asyncio-runner1.2.0indirect
PyPIbackports-tarfile1.2.0indirect
PyPIcertifi2025.4.26indirect
PyPIcffi2.0.0indirect
PyPIcharset-normalizer3.4.2indirect
PyPIcolorama0.4.6indirect
PyPIcoverage7.11.0indirect
PyPIcryptography48.0.1indirect
PyPIdocutils0.22.2indirect
PyPIexceptiongroup1.3.0indirect
PyPIh110.16.0indirect
PyPIhttpcore1.0.9indirect
PyPIhttpx-sse0.4.0indirect
PyPIid1.5.0indirect
PyPIidna3.18indirect
PyPIimportlib-metadata8.7.0indirect
PyPIiniconfig2.1.0indirect
PyPIjaraco-classes3.4.0indirect
PyPIjaraco-context6.0.1indirect
PyPIjaraco-functools4.3.0indirect
PyPIjeepney0.9.0indirect
PyPIjsonschema4.26.0indirect
PyPIjsonschema-specifications2025.9.1indirect
PyPIkeyring25.6.0indirect
PyPImarkdown-it-py4.0.0indirect
PyPImdurl0.1.2indirect
PyPImore-itertools10.8.0indirect
PyPInh30.3.2indirect
PyPInodeenv1.9.1indirect
PyPIpackaging25.0indirect
PyPIpdbe-mcp-server1.1.4indirect
PyPIpluggy1.6.0indirect
PyPIpycparser2.23indirect
PyPIpydantic2.11.5indirect
PyPIpydantic-core2.33.2indirect
PyPIpydantic-settings2.9.1indirect
PyPIpygments2.20.0indirect
PyPIpyjwt2.13.0indirect
PyPIpyright1.1.401indirect
PyPIpytest9.0.3indirect
PyPIpytest-asyncio1.4.0indirect
PyPIpytest-cov7.0.0indirect
PyPIpytest-mock3.15.1indirect
PyPIpython-dotenv1.2.2indirect
PyPIpython-multipart0.0.32indirect
PyPIpytz2026.1.post1indirect
PyPIpywin32312indirect
PyPIpywin32-ctypes0.2.3indirect
PyPIpyyaml6.0.3indirect
PyPIreadme-renderer44.0indirect
PyPIreferencing0.37.0indirect
PyPIrequests-toolbelt1.0.0indirect
PyPIrfc39862.0.0indirect
PyPIrich14.2.0indirect
PyPIrpds-py0.30.0indirect
PyPIrpds-py2026.5.1indirect
PyPIruff0.11.12indirect
PyPIsecretstorage3.4.0indirect
PyPIsniffio1.3.1indirect
PyPIsse-starlette2.3.6indirect
PyPItomli2.2.1indirect
PyPItwine6.2.0indirect
PyPItyping-extensions4.14.0indirect
PyPItyping-inspection0.4.1indirect
PyPIurllib32.7.0indirect
PyPIzipp3.23.0indirect
Raw JSON report machine-readable

Feedback

Spotted something off in this report, or have thoughts to share? Wrong measurements, missed tooling, ideas, questions — anything is welcome. Every message is read and gets a response.

The message is kept through sign-in.

Related records

Inspected repositories sharing catalogue tags or ecosystems with pdbeurope/pdbe-mcp-servers. Read them side by side →

98modelcontextprotocol/python-sdkThe official Python SDK for Model Context Protocol servers and clientsExceptional97langgenius/difyBuild Agentic workflows, RAG pipelines, with rich AI model and tool support on one collaborative workspace. Deploy on cloud, VPC, or self-hosted, so teams move from prototype to production without rebuilding the stack.Exceptional100deepset-ai/haystackOpen-source AI orchestration framework for building context-engineered, production-ready LLM applications. Design modular pipelines and agent workflows with explicit control over retrieval, routing, memory, and generation. Built for scalable agents, RAG, multimodal applications, semantic search, and conversational systems.Exceptional99ag2ai/ag2AG2 (formerly AutoGen): The Open-Source AgentOS.Join us at: https://discord.gg/sNGSwQME3xExceptional98ComposioHQ/composioComposio powers 1000+ toolkits, tool search, context management, authentication, and a sandboxed workbench to help you build AI agents that turn intent into action.Exceptional98intuitem/ciso-assistant-communityCISO Assistant is a one-stop-shop GRC platform for Risk Management, AppSec, Compliance & Audit, TPRM, BIA, Privacy, and Reporting. It supports 200+ global frameworks with automatic control mapping, including ISO 27001, NIST CSF, SOC 2, CIS, PCI DSS, NIS2, DORA, GDPR, HIPAA, CMMC, and more.Exceptional

Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.

Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v2.10.0, schema v0.12.0 — full methodology · metrics wiki.

How one result sits in the wider record: aggregate statistics — PyPI.