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Alphafold

by io.github.pipeworx-io
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Uniprot

uniprot
Read-onlyIdempotent

Fetch AlphaFold structure prediction metadata (PDB/CIF/PAE download URLs, pLDDT scores) by UniProt accession (e.g. "P00533"); equivalent to prediction but takes uniprot_id explicitly.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
uniprot_idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countNo
itemsNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed14 schema fields changed
    • removedOutput schema / properties / alphafoldVersion
      Removed value: -{
-  "description": "AlphaFold version used",
-  "type": "string"
-}
    • addedOutput schema / properties / count
      Added value: +{
+  "type": "number"
+}
    • removedOutput schema / properties / discoveredDate
      Removed value: -{
-  "description": "ISO date when structure was discovered",
-  "type": "string"
-}
    • removedOutput schema / properties / entryId
      Removed value: -{
-  "description": "AlphaFold entry identifier",
-  "type": "string"
-}
    • addedOutput schema / properties / items
      Added value: +{
+  "items": {
+    "properties": {
+      "allVersions": {
+        "items": {
+          "type": "number"
+        },
+        "type": "array"
+      },
+      "amAnnotationsHg19Url": {
+        "type": "string"
+      },
+      "amAnnotationsHg38Url": {
+        "type": "string"
+      },
+      "amAnnotationsUrl": {
+        "type": "string"
+      },
+      "bcifUrl": {
+        "type": "string"
+      },
+      "chainId": {
+        "type": "string"
+      },
+      "cifUrl": {
+        "type": "string"
+      },
+      "entityType": {
+        "type": "string"
+      },
+      "entryId": {
+        "type": "string"
+      },
+      "fractionPlddtConfident": {
+        "type": "number"
+      },
+      "fractionPlddtLow": {
+        "type": "number"
+      },
+      "fractionPlddtVeryHigh": {
+        "type": "number"
+      },
+      "fractionPlddtVeryLow": {
+        "type": "number"
+      },
+      "gene": {
+        "type": "string"
+      },
+      "globalMetricValue": {
+        "type": "number"
+      },
+      "isComplex": {
+        "type": "boolean"
+      },
+      "isReferenceProteome": {
+        "type": "boolean"
+      },
+      "isReviewed": {
+        "type": "boolean"
+      },
+      "isUniProt": {
+        "type": "boolean"
+      },
+      "isUniProtReferenceProteome": {
+        "type": "boolean"
+      },
+      "isUniProtReviewed": {
+        "type": "boolean"
+      },
+      "latestVersion": {
+        "type": "number"
+      },
+      "modelCreatedDate": {
+        "type": "string"
+      },
+      "modelEntityId": {
+        "type": "string"
+      },
+      "msaUrl": {
+        "type": "string"
+      },
+      "organismScientificName": {
+        "type": "string"
+      },
+      "paeDocUrl": {
+        "type": "string"
+      },
+      "paeImageUrl": {
+        "type": "string"
+      },
+      "pdbUrl": {
+        "type": "string"
+      },
+      "plddtDocUrl": {
+        "type": "string"
+      },
+      "providerId": {
+        "type": "string"
+      },
+      "sequence": {
+        "type": "string"
+      },
+      "sequenceChecksum": {
+        "type": "string"
+      },
+      "sequenceEnd": {
+        "type": "number"
+      },
+      "sequenceStart": {
+        "type": "number"
+      },
+      "sequenceVersionDate": {
+        "type": "string"
+      },
+      "taxId": {
+        "type": "number"
+      },
+      "toolUsed": {
+        "type": "string"
+      },
+      "uniprotAccession": {
+        "type": "string"
+      },
+      "uniprotDescription": {
+        "type": "string"
+      },
+      "uniprotEnd": {
+        "type": "number"
+      },
+      "uniprotId": {
+        "type": "string"
+      },
+      "uniprotSequence": {
+        "type": "string"
+      },
+      "uniprotStart": {
+        "type": "number"
+      }
+    },
+    "type": "object"
+  },
+  "type": "array"
+}
    • removedOutput schema / properties / mgnifyId
      Removed value: -{
-  "description": "MGnify identifier",
-  "type": "string"
-}
    • removedOutput schema / properties / modelCreatedDate
      Removed value: -{
-  "description": "ISO date when model was created",
-  "type": "string"
-}
    • removedOutput schema / properties / organism
      Removed value: -{
-  "description": "Organism name",
-  "type": "string"
-}
    • removedOutput schema / properties / plddt
      Removed value: -{
-  "description": "Mean predicted local distance difference test score",
-  "type": "number"
-}
    • removedOutput schema / properties / sequence
      Removed value: -{
-  "description": "Amino acid sequence",
-  "type": "string"
-}
    • removedOutput schema / properties / sequenceLength
      Removed value: -{
-  "description": "Length of protein sequence",
-  "type": "integer"
-}
    • removedOutput schema / properties / structures
      Removed value: -{
-  "description": "Available structure files",
-  "items": {
-    "properties": {
-      "cifUrl": {
-        "description": "CIF format file URL",
-        "type": "string"
-      },
-      "modelPageUrl": {
-        "description": "URL to structure details page",
-        "type": "string"
-      },
-      "modelUrl": {
-        "description": "URL to structure file",
-        "type": "string"
-      },
-      "paeImageUrl": {
-        "description": "PAE image URL",
-        "type": "string"
-      },
-      "paeJsonUrl": {
-        "description": "PAE JSON file URL",
-        "type": "string"
-      },
-      "pdbUrl": {
-        "description": "PDB format file URL",
-        "type": "string"
-      }
-    },
-    "type": "object"
-  },
-  "type": "array"
-}
    • removedOutput schema / properties / uniprotAccession
      Removed value: -{
-  "description": "UniProt accession code",
-  "type": "string"
-}
    • removedOutput schema / properties / uniprotId
      Removed value: -{
-  "description": "UniProt ID",
-  "type": "string"
-}
  2. First observed

TDQS

A4.4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnly, idempotent, openWorld and non-destructive, so the safety profile is covered. The description adds the specific returned content (download URLs and pLDDT scores), which is meaningful beyond structured fields, though it is partially redundant with the existing output schema and says nothing about failures or rate limits.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single sentence that front-loads the payload, then the input, then the sibling equivalence. The parenthetical example costs almost nothing and every clause adds information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Input format, sibling relationship and returned metadata are all covered, and an output schema exists so return values need not be exhaustively spelled out. The only gap is behavioral edge cases (unknown accession, response timing), which are minor for this simple lookup.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0% and the single property is an undescribed string, so the description must compensate — and it does, naming the identifier type (UniProt accession) and giving a concrete example ('P00533'). It is the sole documented input, so one parameter fully accounted for.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb (fetch) and resource (AlphaFold structure prediction metadata) plus the input identifier (UniProt accession) and even the payload fields (PDB/CIF/PAE URLs, pLDDT). It explicitly names the sibling `prediction` in its relationship, so the agent can distinguish the two without opening a schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The clause 'equivalent to `prediction` but takes uniprot_id explicitly' routes the agent: use this when you already hold a UniProt accession, otherwise use `prediction`. Guidance is clear but stops short of an explicit when-not-to-use condition or a stated prerequisite (e.g. what happens with an unknown accession).

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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