io.github.cyanheads/protein-mcp-server
io.github.cyanheads/protein-mcp-server
MCP Bill of Materials
A machine-readable inventory of what this server exposes and depends on: tools with their effects, transports, packages, findings and provenance (schema version 1.0). Third-party text in it is escaped. Also available from the REST API at /api/v1/servers/d6874a26-5a67-4612-8112-430f457732f9/mcbom.
MCP Bill of Materials
root{21}
schema_version: "1.0"
bom_format: "squatch-mcbom"
generator{3}
name: "squatch-mcp"
classifier_version: "rules_v1@2026-10-11.1"
unicode_version: "18.0.0"
server{7}
name: "io.github.cyanheads/protein-mcp-server"
title: null
description: "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models."
version: "0.9.1"
homepage_url: null
source: "official_registry"
upstream_status: "active"
publisher{4}
namespace: "io.github.cyanheads"
display_name: "io.github.cyanheads"
type: "registry_namespace"
status: "unclaimed"
organization: null
repository{5}
url: "https://github.com/cyanheads/protein-mcp-server"
provider: "github"
owner: "cyanheads"
name: "protein-mcp-server"
verified: false
packages[2]
0{4}
registry_type: "npm"
identifier: "@cyanheads/protein-mcp-server"
version: "0.9.1"
transport: "stdio"
1{4}
registry_type: "npm"
identifier: "@cyanheads/protein-mcp-server"
version: "0.9.1"
transport: "streamable-http"
transports[3]
0{5}
kind: "package"
type: "stdio"
endpoint_url: null
endpoint_host: null
auth_type: "unknown"
1{5}
kind: "package"
type: "streamable-http"
endpoint_url: null
endpoint_host: null
auth_type: "unknown"
2{5}
kind: "remote"
type: "streamable-http"
endpoint_url: "https://protein.caseyjhand.com/mcp"
endpoint_host: "protein.caseyjhand.com"
auth_type: "none"
auth{3}
type: "none"
authorization_servers[0]
scopes[0]
protocol{4}
era: "modern"
negotiated_version: "2026-07-28"
supported_versions[0]
transport_type: "streamable-http"
tools[7]
0{9}
name: "protein_analyze_collection"
title: "protein-mcp-server: analyze collection"
effect: "EXECUTE"
effect_confidence: 0.533
capabilities[2]
0{2}
capability: "DATABASE_ACCESS"
confidence: 0.586
1{2}
capability: "PERSONAL_DATA"
confidence: 0.567
risk_severity: "HIGH"
fingerprint: "60d39dcc728f2b5e4632f8ac7480cdb0c8bb1626af22d3ca5f6d9de4b91327cf"
input_schema_fingerprint: "492085eb6e65d5fe5298e1ffbc86aed59effdcb47f9ee499925f5d1bf9d44395"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
1{9}
name: "protein_compare_structures"
title: "protein-mcp-server: compare structures"
effect: "READ"
effect_confidence: 0.711
capabilities[0]
risk_severity: "INFO"
fingerprint: "6991745e6a098016f0a2fa1743ab28b8357b00b93cc1eaa7ae8a2c72b271b36a"
input_schema_fingerprint: "314c8bfb36363ae32044711215dd0ead65ae1aa3d2b5b4f4e5f7500133c3dccd"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
2{9}
name: "protein_find_similar"
title: "protein-mcp-server: find similar"
effect: "READ"
effect_confidence: 0.813
capabilities[1]
0{2}
capability: "DATABASE_ACCESS"
confidence: 0.852
risk_severity: "INFO"
fingerprint: "947bec94a2f573b0a15a0668f3460a3b66205a7b325daeb6b187622b932bb79d"
input_schema_fingerprint: "290a683f4b0bc195e6853379004233a709480882214dacae3c43b3b126ee8661"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
3{9}
name: "protein_get_annotations"
title: "protein-mcp-server: get annotations"
effect: "READ"
effect_confidence: 0.66
capabilities[0]
risk_severity: "INFO"
fingerprint: "9d8ef62107ab4f869d47cbd41f6f8896ec1e0b4efd62e6f29bba049286f6c49c"
input_schema_fingerprint: "db2857b94bf05d6ed62a2297f3f6f038ccfbd5d86403dc9210ff732556f17005"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
4{9}
name: "protein_get_structure"
title: "protein-mcp-server: get structure"
effect: "READ"
effect_confidence: 0.841
capabilities[2]
0{2}
capability: "FILE_ACCESS"
confidence: 0.632
1{2}
capability: "LOCATION"
confidence: 0.864
risk_severity: "LOW"
fingerprint: "ab46c6b061a82e74cc42b5a1ddcab35fa4b3c327e70983b19a755e941f2a6f52"
input_schema_fingerprint: "9cab8c749739fc943d806f4cc07f1433b7a1e247df6506c45f8c4c55b981f984"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
5{9}
name: "protein_search_structures"
title: "protein-mcp-server: search structures"
effect: "READ"
effect_confidence: 0.841
capabilities[0]
risk_severity: "INFO"
fingerprint: "991fb145e9bdf66f5a960d34482282f40114168bd6c0ab84f1991118249339ee"
input_schema_fingerprint: "adc52b466a7e812fddf95fb22a6f2832e8a0d3966aa00a1d161c2ad024da3b4b"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
6{9}
name: "protein_track_ligands"
title: "protein-mcp-server: track ligands"
effect: "READ"
effect_confidence: 0.32
capabilities[1]
0{2}
capability: "LOCATION"
confidence: 0.724
risk_severity: "LOW"
fingerprint: "826707e483171c0bfb41e0acf2f48c08a2e0a70f458e180de4334ef4299c86d2"
input_schema_fingerprint: "cd2f0024567d9cff42507b234fb39aa6730a8f0725b4594b72b4b4dd44974d60"
annotations{5}
title: null
readOnlyHint: true
destructiveHint: null
idempotentHint: null
openWorldHint: true
resources[4]
0{4}
key: "skill://protein-guide/SKILL.md"
kind: "resource"
mime_type: "text/markdown"
fingerprint: "3ed8b45d1aa44d2588d715ae7bbe8dbe7051662f45add77b7f631cafcbafd952"
1{4}
key: "af://{uniprot}"
kind: "template"
mime_type: "application/json"
fingerprint: "19ac5613fdaf9ef6725f1dbc9409f3bc5b4addbd8c6c72625eaaba15f6a10634"
2{4}
key: "pdb://{entry_id}"
kind: "template"
mime_type: "application/json"
fingerprint: "7e7b5514539fa82c5a5ae5975c1155d83c43f5610b36c99246d55e9a8f46b559"
3{4}
key: "skill://{+path}"
kind: "template"
mime_type: null
fingerprint: "9777dc7f1cf468158c157032a0ccebf9b50270f4e8753af9ccaf2fe99890ccf0"
prompts[0]
extensions[1]
0: "io.modelcontextprotocol/skills"
data{6}
privacy_completeness: "not_provided"
data_categories[0]
ai_training: null
retention_policy: null
processing_regions[0]
subprocessors[0]
external_integrations[1]
0{3}
host: "protein.caseyjhand.com"
registrable_domain: "caseyjhand.com"
source: "transport"
findings[5]
0{6}
check_id: "SQ-SERVER-AUTH-NONE-WRITE"
category: "authentication"
severity: "MEDIUM"
title: "State-changing tools available without authentication"
subject_type: "server"
subject_name: null
1{6}
check_id: "SQ-TOOL-ANNOTATION-UNDERCLAIM"
category: "annotations"
severity: "MEDIUM"
title: "Annotations understate what the tool does"
subject_type: "tool"
subject_name: "protein_analyze_collection"
2{6}
check_id: "SQ-TOOL-CONCEALMENT"
category: "prompt_injection"
severity: "HIGH"
title: "Text asks the AI model to hide actions from the user"
subject_type: "tool"
subject_name: "protein_analyze_collection"
3{6}
check_id: "SQ-TOOL-CONCEALMENT"
category: "prompt_injection"
severity: "HIGH"
title: "Text asks the AI model to hide actions from the user"
subject_type: "tool"
subject_name: "protein_find_similar"
4{6}
check_id: "SQ-TOOL-TITLE-EFFECT-MISMATCH"
category: "deceptive_metadata"
severity: "HIGH"
title: "Display title describes a lower-impact action than the name"
subject_type: "tool"
subject_name: "protein_analyze_collection"
trust{9}
registry_namespace: "verified_upstream"
publisher_identity: "unverified"
organization: "unverified"
domain: "unverified"
repository: "unverified"
source_provenance: "partial"
security_scan: "findings_detected"
privacy_transparency: "not_provided"
monitoring: "active"
provenance{4}
registry_name: "io.github.cyanheads/protein-mcp-server"
registry_content_sha256: "601e10c72e517b58867f5a4d421ad98afef75327bb5653e2ad576fefdb0a8845"
scan_snapshot_fingerprint: "f6267f2c795f83699dbf49bb8260d53a69bdcb18f96a9b230355e7741035fa46"
scanner_version: "1.0.0"
timestamps{4}
generated_at: "2026-11-15T02:14:26.850Z"
observed_at: "2026-11-15T00:29:55.921+00:00"
registry_published_at: "2026-11-14T22:14:32.752757+00:00"
registry_updated_at: null