foldseek-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| FOLDSEEK_MCP_RUN_ROOT | No | Path to the root directory for search job outputs. | |
| FOLDSEEK_MCP_MODEL_ROOT | No | Path to the root directory for FoldSeek models (e.g., ProstT5). | |
| FOLDSEEK_MCP_AUTO_DOWNLOAD | No | Enable automatic download of missing databases and models. Set to 'true' or 'false'. | |
| FOLDSEEK_MCP_DATABASE_ROOT | No | Path to the root directory for FoldSeek databases. | |
| FOLDSEEK_MCP_FOLDSEEK_BINARY | No | Path to the FoldSeek binary executable. If not set, the server looks for bundled or system-installed FoldSeek. | |
| FOLDSEEK_MCP_ALLOWED_INPUT_ROOTS | No | Comma-separated list of allowed root directories for input file paths. | |
| FOLDSEEK_MCP_MAX_AUTO_DOWNLOAD_GB | No | Maximum size in GB for automatic downloads. If the download exceeds this limit, it requires confirmation. |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
| logging | {} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| extensions | {
"io.modelcontextprotocol/ui": {}
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| foldseek_search_structureC | Run FoldSeek easy-search with a PDB/mmCIF structure query. |
| foldseek_search_sequenceC | Run FoldSeek easy-search with a FASTA query and configured ProstT5 model. |
| foldseek_list_databasesA | List installed and available FoldSeek databases and model resources. |
| foldseek_download_databaseC | Download or prepare a catalog-listed FoldSeek database. |
| foldseek_validate_environmentA | Validate the local FoldSeek MCP runtime environment. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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