PatSnap Biology Modality
About
PatSnap Biology Modality MCP is a Model Context Protocol server that equips AI agents with direct, structured access to biological sequence data, modification records, and antibody-antigen interactions. It enables sequence similarity searching, post-translational modification que
Details
- Transport
- SSE
Explore
- Provides structured access to biological sequence data and modifications
- Supports antibody-antigen interaction queries
- Enables sequence similarity searching across 200M+ records
- Allows post-translational modification (PTM) querying
- Facilitates antibody discovery from patents and literature
- Uses streamable HTTP transport for real-time requests
Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
PatSnap Biology ModalityCommand (node, npx, python, etc.)Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
``json``
{
"mcpServers": {
"patsnap-biology-modality": {
"url": "https://connect.patsnap.com/06e741/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}
}
ls_sequence_search_submit
Submit a sequence search job. Use this tool when the user wants to launch a bio sequence search job. The Python service only validates the request shape and forwards the payload to the downstream Java MCP resource. Tool flow: 1. Call this tool `ls_sequence_search_submit` to submit the job and get `job_id`. 2. Call `ls_sequence_search_check_status` with `job_id` to poll backend status. 3. After the status becomes success, call `ls_sequence_search_get_results` with `job_id`…
ls_sequence_search_check_status
Get the current execution status. Use this tool after `ls_sequence_search_submit` or `ls_modification_search_submit` to check the current backend status of a submitted job. Args: job_id: str, backend search job ID Returns: Dict[str, Any]: Response body: { "status": "SUCCESS" } - status: backend job status string, commonly SUCCESS, RUNNING, or FAILED.
ls_sequence_search_get_results
Get paged results. Use this tool after `ls_sequence_search_check_status` reports success for a job created by `ls_sequence_search_submit` or `ls_modification_search_submit`. It retrieves the result page directly returned by the downstream Java MCP resource. Args: job_id: str, backend search job ID offset: int, result offset starting from 0 limit: int, page size for the downstream query sort_field: str, optional sorting field order: str, optional sorting order, supports "…
ls_sequence_alignment
Run sequence alignment. Use this tool when the user wants to align biological sequences directly. The Python service validates the request shape and forwards the payload to the downstream Java MCP resource. Args: sequence_type: str, sequence type, supports "NUCLEOTIDE" and "PROTEIN" alignment_type: str, alignment type, supports "PSA" for pairwise sequence alignment and "MSA" for multiple sequence alignment sequences: List[str], target sequences for PSA, or all sequences …
ls_sequence_fetch
Fetch sequence details in batch. Batch fetch full detail records by sequence number. Args: sequence_numbers: List[int]. Sequence number list used to fetch sequence details. Each item must be an integer. Returns: Dict[str, Any]: Response body: { "items": [ { "sequence_number": 1, "length": 332, "sequence_type": "PROTEIN", "organism": ["Bombus terrestris", "unidentified"], "is_…
ls_patent_sequence_fetch
Fetch patent-related sequence details. Fetch sequences associated with a patent by patent ID or patent number. Args: patent_id: str, patent ID used to fetch related sequences. pn: str, patent number used to resolve patent ID before fetching sequences. offset: int, pagination offset, starting from 0. limit: int, page size. Must be between 1 and 100. Returns: Dict[str, Any]: Response body: { "total": 85, "items": [ { …
ls_modification_search_submit
Submit a modification search job. Use this tool when the user wants to search bio sequence records by modification conditions and optionally narrow the result set with sequence length or a query sequence. The Python service validates the request shape and forwards the payload to the downstream Java MCP resource. Tool flow: 1. Call this tool `ls_modification_search_submit` to submit the job and get `job_id`. 2. Call `ls_sequence_search_check_status` with `job_id` to poll backend stat…
ls_antibody_antigen_search
Search antibody-antigen relations. IMPORTANT: You must provide `target_name` as a search parameter. Use this tool when the user wants to find antibodies associated with a target antigen and optionally narrow the result set with facet filters. The Python service only validates the request shape and forwards the payload to the downstream Java MCP resource. Args: target_name: str, antigen target name used for exact or keyword lookup offset: int, pagination offset, starting from 0 l…
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"patsnap biology modality": {
"patsnap-biology-modality": {
"url": "https://connect.patsnap.com/06e741/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}
}
}McpServers
{
"patsnap-biology-modality": {
"url": "https://connect.patsnap.com/06e741/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}Server Config
``json
{
"mcpServers": {
"patsnap-biology-modality": {
"url": "https://connect.patsnap.com/06e741/logic-mcp?apikey=YOUR_API_KEY",
"type": "streamableHttp"
}
}
}
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