{
  "project_id": "PDBeurope/PDBe-MCP-Servers",
  "repo": "PDBeurope/PDBe-MCP-Servers",
  "name": "PDBe-MCP-Servers",
  "github_url": "https://github.com/PDBeurope/PDBe-MCP-Servers",
  "homepage_url": null,
  "language": "Python",
  "license": "Apache-2.0",
  "project_kind": "project",
  "category": [
    "mcp_server"
  ],
  "tags": [
    "ai-integration",
    "api-server",
    "bioinformatics",
    "knowledge-graph",
    "llm-tools",
    "mcp",
    "pdbe",
    "protein-structures",
    "python",
    "structural-biology"
  ],
  "description": "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.",
  "overview": "Use PDBeurope/PDBe-MCP-Servers when the user needs a mcp server project with library-only, local, cloud deployment options.",
  "alternatives": [
    {
      "repo": "headroomlabs-ai/headroom",
      "reason": "Same mcp server intent with mcp overlap."
    },
    {
      "repo": "rocketride-org/rocketride-server",
      "reason": "Same mcp server intent with mcp overlap."
    },
    {
      "repo": "AstrBotDevs/AstrBot",
      "reason": "Same mcp server intent with mcp overlap."
    }
  ],
  "related": [
    {
      "repo": "unclecode/crawl4ai",
      "reason": "Related to PDBeurope/PDBe-MCP-Servers through mcp server category and library_only deployment."
    },
    {
      "repo": "deepset-ai/haystack",
      "reason": "Related to PDBeurope/PDBe-MCP-Servers through mcp server category and library_only deployment."
    },
    {
      "repo": "googleapis/mcp-toolbox",
      "reason": "Related to PDBeurope/PDBe-MCP-Servers through mcp server category and library_only deployment."
    },
    {
      "repo": "bytechefhq/bytechef",
      "reason": "Related to PDBeurope/PDBe-MCP-Servers through mcp server category and library_only deployment."
    },
    {
      "repo": "ThreatRecall/zettelforge",
      "reason": "Related to PDBeurope/PDBe-MCP-Servers through mcp server category and library_only deployment."
    },
    {
      "repo": "1jehuang/jcode",
      "reason": "Related to PDBeurope/PDBe-MCP-Servers through mcp server category and library_only deployment."
    },
    {
      "repo": "QwenLM/qwen-code",
      "reason": "Related to PDBeurope/PDBe-MCP-Servers through mcp server category and library_only deployment."
    },
    {
      "repo": "lastmile-ai/mcp-agent",
      "reason": "Related to PDBeurope/PDBe-MCP-Servers through mcp server category and library_only deployment."
    }
  ],
  "dependencies": [
    "MCP",
    "LLM provider"
  ],
  "deployments": [
    "library_only",
    "local",
    "cloud"
  ],
  "difficulty": "beginner",
  "cloudflare_ready": false,
  "use_cases": [
    "connect agents to tools",
    "expose APIs through MCP",
    "bootstrap MCP integrations"
  ],
  "not_good_for": [
    "edge-only Cloudflare Workers deployment without adaptation",
    "users expecting a complete hosted product"
  ],
  "classification": {
    "category": {
      "confidence": "high",
      "evidence": [
        "Matched \"model context protocol\" in metadata.",
        "Matched \"mcp server\" in metadata.",
        "Matched \"mcp\" in metadata."
      ]
    },
    "deployment": {
      "confidence": "high",
      "evidence": [
        "Matched \"pip install\" in repository content.",
        "Local usage is assumed for open source repositories unless contradicted."
      ]
    },
    "difficulty": {
      "confidence": "medium",
      "evidence": [
        "Repository has under 10k stars, so complexity is treated conservatively."
      ]
    },
    "cloudflare_ready": {
      "confidence": "high",
      "evidence": [
        "Runtime blocker: python.",
        "No Cloudflare deployment signal detected.",
        "No wrangler.toml found in inspected repository files."
      ]
    }
  },
  "quality_signals": {
    "stars": 39,
    "recent_commits": 0,
    "contributors": 2,
    "issue_response_time_hours": null,
    "release_frequency_180d": 12
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  "quality_signal_confidence": {
    "stars_30d_delta": "snapshot",
    "stars30d_window_days": 34,
    "commits_30d": "complete",
    "releases_180d": "complete",
    "contributors_90d": "complete"
  },
  "quality_score": 19,
  "agent_score": 57,
  "score": 67,
  "agent_score_breakdown": {
    "documentation": 90,
    "maintenance": 32,
    "deployment": 80,
    "popularity": 32,
    "community": 47
  },
  "git_top_score": 67,
  "git_top_score_breakdown": {
    "community": 64,
    "maintenance": 34,
    "documentation": 92,
    "stability": 85,
    "adoption": 35,
    "agent_readability": 100
  },
  "verification": {
    "schema_version": "git-top.verification.v1",
    "overall_status": "partial",
    "observed_at": "2026-09-26T07:01:07.098Z",
    "signals": {
      "activity": {
        "status": "observed",
        "source": "github_metadata",
        "evidence": [
          "project.pushed_at",
          "metrics.recent_push_days"
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      },
      "license": {
        "status": "observed",
        "source": "github_metadata",
        "evidence": [
          "project.license"
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      "documentation": {
        "status": "observed",
        "source": "github_metadata",
        "evidence": [
          "project.description"
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      "runtime": {
        "status": "inferred",
        "source": "git_top_heuristic",
        "evidence": [
          "agent_card.deployment",
          "agent_card.cloudflare_ready"
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      "install": {
        "status": "not_run",
        "source": "git_top_runtime",
        "evidence": [
          "installation/build probe is not enabled"
        ]
      },
      "security": {
        "status": "not_run",
        "source": "git_top_runtime",
        "evidence": [
          "dependency/security scan is not enabled"
        ]
      },
      "mcp": {
        "status": "not_run",
        "source": "git_top_runtime",
        "evidence": [
          "MCP liveness and tool-call probe is not enabled"
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      }
    },
    "coverage": {
      "observed": 3,
      "inferred": 1,
      "not_run": 3,
      "unknown": 0
    },
    "next_steps": [
      "Run an installation/build probe before production adoption.",
      "Run a dependency and security scan before treating the score as a trust claim.",
      "Run MCP initialize, tools/list, first-call, and error probes before relying on this server."
    ]
  },
  "summary": {
    "tl_dr": "Use PDBeurope/PDBe-MCP-Servers when the user needs a mcp server project with library-only, local, cloud deployment options.",
    "purpose": "Use PDBeurope/PDBe-MCP-Servers when the user needs a mcp server project with library-only, local, cloud deployment options.",
    "install": "Install as a library or package using the repository instructions.",
    "inputs": [
      "tool definitions",
      "resource config",
      "transport settings"
    ],
    "outputs": [
      "MCP tools",
      "JSON-RPC responses",
      "server capabilities"
    ],
    "good_for": [
      "connect agents to tools",
      "expose APIs through MCP",
      "bootstrap MCP integrations",
      "agent tool exposure",
      "MCP integrations",
      "tool servers"
    ],
    "not_good_for": [
      "edge-only Cloudflare Workers deployment without adaptation",
      "users expecting a complete hosted product",
      "front-end apps",
      "non-tooling backends"
    ],
    "deployment": [
      "library_only",
      "local",
      "cloud"
    ],
    "alternatives": [
      {
        "repo": "headroomlabs-ai/headroom",
        "reason": "Same mcp server intent with mcp overlap."
      },
      {
        "repo": "rocketride-org/rocketride-server",
        "reason": "Same mcp server intent with mcp overlap."
      },
      {
        "repo": "AstrBotDevs/AstrBot",
        "reason": "Same mcp server intent with mcp overlap."
      }
    ]
  },
  "evidence": {
    "classification": {
      "category": {
        "confidence": "high",
        "evidence": [
          "Matched \"model context protocol\" in metadata.",
          "Matched \"mcp server\" in metadata.",
          "Matched \"mcp\" in metadata."
        ]
      },
      "deployment": {
        "confidence": "high",
        "evidence": [
          "Matched \"pip install\" in repository content.",
          "Local usage is assumed for open source repositories unless contradicted."
        ]
      },
      "difficulty": {
        "confidence": "medium",
        "evidence": [
          "Repository has under 10k stars, so complexity is treated conservatively."
        ]
      },
      "cloudflare_ready": {
        "confidence": "high",
        "evidence": [
          "Runtime blocker: python.",
          "No Cloudflare deployment signal detected.",
          "No wrangler.toml found in inspected repository files."
        ]
      }
    },
    "quality_signal_confidence": {
      "stars_30d_delta": "snapshot",
      "stars30d_window_days": 34,
      "commits_30d": "complete",
      "releases_180d": "complete",
      "contributors_90d": "complete"
    },
    "verification": {
      "schema_version": "git-top.verification.v1",
      "overall_status": "partial",
      "observed_at": "2026-09-26T07:01:07.098Z",
      "signals": {
        "activity": {
          "status": "observed",
          "source": "github_metadata",
          "evidence": [
            "project.pushed_at",
            "metrics.recent_push_days"
          ]
        },
        "license": {
          "status": "observed",
          "source": "github_metadata",
          "evidence": [
            "project.license"
          ]
        },
        "documentation": {
          "status": "observed",
          "source": "github_metadata",
          "evidence": [
            "project.description"
          ]
        },
        "runtime": {
          "status": "inferred",
          "source": "git_top_heuristic",
          "evidence": [
            "agent_card.deployment",
            "agent_card.cloudflare_ready"
          ]
        },
        "install": {
          "status": "not_run",
          "source": "git_top_runtime",
          "evidence": [
            "installation/build probe is not enabled"
          ]
        },
        "security": {
          "status": "not_run",
          "source": "git_top_runtime",
          "evidence": [
            "dependency/security scan is not enabled"
          ]
        },
        "mcp": {
          "status": "not_run",
          "source": "git_top_runtime",
          "evidence": [
            "MCP liveness and tool-call probe is not enabled"
          ]
        }
      },
      "coverage": {
        "observed": 3,
        "inferred": 1,
        "not_run": 3,
        "unknown": 0
      },
      "next_steps": [
        "Run an installation/build probe before production adoption.",
        "Run a dependency and security scan before treating the score as a trust claim.",
        "Run MCP initialize, tools/list, first-call, and error probes before relying on this server."
      ]
    },
    "source_fields": [
      "project.description",
      "project.topics",
      "project.language",
      "project.license",
      "agent_card.summary_for_agent",
      "agent_card.use_cases",
      "agent_card.deployment",
      "agent_card.classification",
      "metrics",
      "verification.signals"
    ],
    "caveats": [
      "edge-only Cloudflare Workers deployment without adaptation",
      "users expecting a complete hosted product",
      "Independent installation, security, or runtime probes have not been run for this project."
    ],
    "confidence_reason": "Classification evidence and quality signals are strong enough for shortlist reasoning when metadata is current.",
    "last_verified_at": "2026-09-26T07:01:07.098Z"
  },
  "caveats": [
    "edge-only Cloudflare Workers deployment without adaptation",
    "users expecting a complete hosted product",
    "Independent installation, security, or runtime probes have not been run for this project."
  ],
  "confidence_reason": "Classification evidence and quality signals are strong enough for shortlist reasoning when metadata is current.",
  "source_fields": [
    "project.description",
    "project.topics",
    "project.language",
    "project.license",
    "agent_card.summary_for_agent",
    "agent_card.use_cases",
    "agent_card.deployment",
    "agent_card.classification",
    "metrics",
    "verification.signals"
  ],
  "last_verified_at": "2026-09-26T07:01:07.098Z",
  "knowledge": {
    "project": {
      "id": "PDBeurope/PDBe-MCP-Servers",
      "owner": "PDBeurope",
      "name": "PDBe-MCP-Servers",
      "full_name": "PDBeurope/PDBe-MCP-Servers",
      "github_url": "https://github.com/PDBeurope/PDBe-MCP-Servers",
      "homepage_url": null,
      "description": "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.",
      "language": "Python",
      "topics": [
        "ai-integration",
        "api-server",
        "bioinformatics",
        "knowledge-graph",
        "llm-tools",
        "mcp",
        "pdbe",
        "protein-structures",
        "python",
        "structural-biology"
      ],
      "license": "Apache-2.0",
      "stars": 39,
      "forks": 1,
      "open_issues": 3,
      "default_branch": "main",
      "created_at": "2025-06-08T17:04:48Z",
      "updated_at": "2026-09-09T14:59:38Z",
      "pushed_at": "2026-07-29T15:08:59Z",
      "synced_at": "2026-09-26T07:01:07.098Z"
    },
    "agent_card": {
      "project_id": "PDBeurope/PDBe-MCP-Servers",
      "project_kind": "project",
      "category": "mcp_server",
      "difficulty": "beginner",
      "deployment": [
        "library_only",
        "local",
        "cloud"
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      "cloudflare_ready": false,
      "use_cases": [
        "connect agents to tools",
        "expose APIs through MCP",
        "bootstrap MCP integrations"
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        "edge-only Cloudflare Workers deployment without adaptation",
        "users expecting a complete hosted product"
      ],
      "alternatives": [
        {
          "project_id": "headroomlabs-ai/headroom",
          "reason": "Same mcp server intent with mcp overlap."
        },
        {
          "project_id": "rocketride-org/rocketride-server",
          "reason": "Same mcp server intent with mcp overlap."
        },
        {
          "project_id": "AstrBotDevs/AstrBot",
          "reason": "Same mcp server intent with mcp overlap."
        }
      ],
      "summary_for_agent": "Use PDBeurope/PDBe-MCP-Servers when the user needs a mcp server project with library-only, local, cloud deployment options.",
      "classification": {
        "category": {
          "confidence": "high",
          "evidence": [
            "Matched \"model context protocol\" in metadata.",
            "Matched \"mcp server\" in metadata.",
            "Matched \"mcp\" in metadata."
          ]
        },
        "deployment": {
          "confidence": "high",
          "evidence": [
            "Matched \"pip install\" in repository content.",
            "Local usage is assumed for open source repositories unless contradicted."
          ]
        },
        "difficulty": {
          "confidence": "medium",
          "evidence": [
            "Repository has under 10k stars, so complexity is treated conservatively."
          ]
        },
        "cloudflare_ready": {
          "confidence": "high",
          "evidence": [
            "Runtime blocker: python.",
            "No Cloudflare deployment signal detected.",
            "No wrangler.toml found in inspected repository files."
          ]
        }
      },
      "schema_version": "v1",
      "generated_at": "2026-09-26T07:01:07.098Z"
    },
    "metrics": {
      "project_id": "PDBeurope/PDBe-MCP-Servers",
      "stars_30d_delta": 2,
      "commits_30d": 0,
      "releases_180d": 12,
      "contributors_90d": 2,
      "issue_first_response_median_hours": null,
      "recent_push_days": 58,
      "git_score": 19,
      "maintenance_score": 32,
      "signal_confidence": {
        "stars_30d_delta": "snapshot",
        "stars30d_window_days": 34,
        "commits_30d": "complete",
        "releases_180d": "complete",
        "contributors_90d": "complete"
      },
      "calculated_at": "2026-09-26T07:01:07.098Z"
    }
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  "resolved_from": {
    "requested_id": "PDBeurope/PDBe-MCP-Servers",
    "resolved_id": "PDBeurope/PDBe-MCP-Servers",
    "resolution": "direct"
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  "metadata": {
    "source": "d1",
    "reason": "d1_query",
    "project_count": 1213,
    "generated_at": "2026-09-26T16:51:14.428Z",
    "snapshot_id": "d1:1213:2026-09-26T16:31:17.417Z",
    "latest_synced_at": "2026-09-26T16:31:17.417Z",
    "schema_version": "git-top.knowledge.v1",
    "loaded_project_limit": 2000,
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}