PDB Entry Publications: Papers, DOIs and PubMed IDs Behind a Protein Structure (PDBe)

pdbe/entry-publications

Publications associated with one Protein Data Bank entry by its four-character PDB id: title, DOI, PubMed id, journal, volume, pages, year, abstract sections where available and the author list. Several publications can be listed, and many fields are null when the source does not have them. Returned as the PDBe response, keyed by the PDB id. Protein Data Bank in Europe data (PDB archive data is CC0), served by Eden Engine; not an official PDBe product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $5.

Data source

Protein Data Bank in Europe (PDBe), EMBL-EBI

Data from the Protein Data Bank in Europe (PDBe), EMBL-EBI. PDB archive data is CC0 1.0 (wwpdb.org/about/usage-policies); PDBe-added annotation is CC BY 4.0. Served by Eden Engine; not an official PDBe product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

Connect once and your AI can find and run this tool, and any other it needs.

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agent

// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "pdbe/entry-publications" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "pdbe/entry-publications" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "pdbe/entry-publications", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "pdbe/entry-publications", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

Not connected yet? Point your MCP client at https://mcp.eden-engine.com/mcp, then copy a config for your client.

Pricing

Every charge this tool can incur.

Charge	Price
Per call	$0.0026

Updated: Oct 20, 2026

Input and output schemas

Input schema

input_schema.json

{
  "type": "object",
  "required": [
    "pdb_id"
  ],
  "properties": {
    "pdb_id": {
      "type": "string",
      "pattern": "^[0-9][a-z0-9]{3}$",
      "description": "Four-character PDB id in lowercase: a digit followed by three lowercase letters or digits, for example 1cbs."
    }
  },
  "additionalProperties": false
}

Output schema

output_schema.json

{
  "type": "object",
  "description": "The PDBe response, keyed by the lowercase PDB id you asked for. The value is a list with one record per publication.",
  "minProperties": 1,
  "additionalProperties": {
    "type": "array",
    "items": {
      "type": "object",
      "properties": {
        "doi": {
          "type": [
            "string",
            "null"
          ]
        },
        "type": {
          "type": [
            "string",
            "null"
          ],
          "description": "For example J for a journal article."
        },
        "title": {
          "type": [
            "string",
            "null"
          ]
        },
        "abstract": {
          "type": "object",
          "description": "Abstract split into background, objective, methods, results, conclusions and unassigned; any may be null.",
          "additionalProperties": {
            "type": [
              "string",
              "null"
            ]
          }
        },
        "pubmed_id": {
          "type": [
            "string",
            "null"
          ]
        },
        "author_list": {
          "type": "array",
          "items": {
            "type": "object",
            "properties": {
              "initials": {
                "type": [
                  "string",
                  "null"
                ]
              },
              "full_name": {
                "type": "string"
              },
              "last_name": {
                "type": [
                  "string",
                  "null"
                ]
              }
            },
            "additionalProperties": true
          }
        },
        "journal_info": {
          "type": "object",
          "properties": {
            "year": {
              "type": [
                "integer",
                "null"
              ]
            },
            "issue": {
              "type": [
                "string",
                "null"
              ]
            },
            "pages": {
              "type": [
                "string",
                "null"
              ]
            },
            "volume": {
              "type": [
                "string",
                "null"
              ]
            },
            "ISO_abbreviation": {
              "type": [
                "string",
                "null"
              ]
            },
            "pdb_abbreviation": {
              "type": [
                "string",
                "null"
              ]
            }
          },
          "additionalProperties": true
        },
        "associated_entries": {
          "type": [
            "string",
            "null"
          ],
          "description": "Other PDB ids sharing this publication, as one comma-separated string."
        }
      },
      "additionalProperties": true
    }
  }
}