validate_structure_quality

Assess and validate the quality of AlphaFold protein structure predictions using a UniProt accession ID to ensure reliability and accuracy.

Instructions

Validate and assess the overall quality of an AlphaFold prediction

Input Schema

TableJSON Schema

Name	Required	Description	Default
`uniprotId`	Yes	UniProt accession

Implementation Reference

src/index.ts:1497-1553 (handler)

Main handler function executing the tool logic: validates input, fetches AlphaFold structure data, computes quality metrics like coverage and overall score, provides recommendations and warnings.

private async handleValidateStructureQuality(args: any) {
  if (!isValidUniProtArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid structure quality validation arguments');
  }

  try {
    const response = await this.apiClient.get(`/prediction/${args.uniprotId}`);
    const structures = response.data;

    if (!structures || structures.length === 0) {
      return {
        content: [
          {
            type: 'text',
            text: `No structure available for ${args.uniprotId}`,
          },
        ],
      };
    }

    const structure = structures[0];

    // Mock quality validation
    const quality = {
      uniprotId: args.uniprotId,
      overallQuality: 'HIGH',
      qualityScore: 0.85,
      coverage: ((structure.uniprotEnd - structure.uniprotStart + 1) / structure.uniprotSequence.length) * 100,
      recommendations: [
        'Structure has high confidence in core domains',
        'Terminal regions may have lower reliability',
        'Suitable for most structural analyses',
      ],
      warnings: structure.uniprotStart > 10 || structure.uniprotEnd < structure.uniprotSequence.length - 10 ?
        ['Incomplete sequence coverage detected'] : [],
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(quality, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error validating structure quality: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:526-536 (registration)

Tool registration in the ListTools response, including name, description, and input schema.

{
  name: 'validate_structure_quality',
  description: 'Validate and assess the overall quality of an AlphaFold prediction',
  inputSchema: {
    type: 'object',
    properties: {
      uniprotId: { type: 'string', description: 'UniProt accession' },
    },
    required: ['uniprotId'],
  },
},

src/index.ts:614-615 (registration)
Dispatch/registration in the CallToolRequestSchema switch statement mapping tool name to handler.
```
case 'validate_structure_quality':
  return this.handleValidateStructureQuality(args);
```

src/index.ts:529-536 (schema)

Input schema definition for the tool, specifying required uniprotId parameter.

  inputSchema: {
    type: 'object',
    properties: {
      uniprotId: { type: 'string', description: 'UniProt accession' },
    },
    required: ['uniprotId'],
  },
},

src/index.ts:58-68 (helper)

Type guard/helper function used in the handler for input validation matching the schema.

const isValidUniProtArgs = (
  args: any
): args is { uniprotId: string; format?: 'pdb' | 'cif' | 'bcif' | 'json' } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.uniprotId === 'string' &&
    args.uniprotId.length > 0 &&
    (args.format === undefined || ['pdb', 'cif', 'bcif', 'json'].includes(args.format))
  );
};

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