get_protein_features

Retrieve functional features and domains for a protein using its UniProt accession number to analyze protein structure and biological roles.

Instructions

Get functional features and domains for a protein

Input Schema

TableJSON Schema

Name	Required	Description	Default
`accession`	Yes	UniProt accession number

Implementation Reference

src/index.ts:946-988 (handler)

The handler function for 'get_protein_features' tool. Fetches protein data from UniProt API and extracts specific features like domains, active sites, binding sites, comments, and keywords.

private async handleGetProteinFeatures(args: any) {
  if (!isValidProteinInfoArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid protein features arguments');
  }

  try {
    const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, {
      params: { format: 'json' },
    });

    // Extract features and domains from the response
    const protein = response.data;
    const features = {
      accession: protein.primaryAccession,
      name: protein.uniProtkbId,
      features: protein.features || [],
      comments: protein.comments || [],
      keywords: protein.keywords || [],
      domains: protein.features?.filter((f: any) => f.type === 'Domain') || [],
      activeSites: protein.features?.filter((f: any) => f.type === 'Active site') || [],
      bindingSites: protein.features?.filter((f: any) => f.type === 'Binding site') || [],
    };

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

src/index.ts:737-737 (registration)
Tool dispatch/registration in the CallToolRequestSchema switch statement.
```
return this.handleGetProteinFeatures(args);
```

src/index.ts:452-460 (schema)

Tool schema and metadata registration in the ListToolsRequestSchema response.

name: 'get_protein_features',
description: 'Get functional features and domains for a protein',
inputSchema: {
  type: 'object',
  properties: {
    accession: { type: 'string', description: 'UniProt accession number' },
  },
  required: ['accession'],
},

src/index.ts:79-89 (helper)

Validation helper function used by get_protein_features to validate input arguments.

const isValidProteinInfoArgs = (
  args: any
): args is { accession: string; format?: string } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.accession === 'string' &&
    args.accession.length > 0 &&
    (args.format === undefined || ['json', 'tsv', 'fasta', 'xml'].includes(args.format))
  );
};

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