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. |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| 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 | |
TDQS
Scored across 5 tools
Each tool targets a distinct operation: database download, listing, sequence search, structure search, and environment validation. No functional overlap.
All tools follow the consistent pattern 'foldseek_verb_noun' with clear, descriptive names (e.g., foldseek_download_database, foldseek_search_sequence).
Five tools is appropriate for a focused scientific server covering database management, two search modalities, and environment checks.
Core workflows are covered, but missing a tool to delete or update databases, which is a minor gap for full lifecycle management.