> ## Documentation Index > Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt > Use this file to discover all available pages before exploring further. # Server Functions > Reference for the functions the proto-tools MCP server exposes to an agent The server exposes seven functions, plus `deploy_tool` when it runs against Modal, where you deploy tools yourself. They are grouped below by what the agent is doing: checking the workspace, discovering a tool, inspecting its contract, running it, and deploying one that is not available yet. Large outputs such as predicted structures and embeddings are written to disk and returned as file paths rather than inline, so a result never floods the agent's context. MCP calls these functions *tools*, and a client such as Claude Code lists them under that name. This page calls them functions so they stay distinct from the bioinformatics tools they operate on, which is the sense `tool_key` and `list_tools` already use. A `tool_key` that matches nothing is returned as a result rather than an error, carrying `did_you_mean` suggestions and a reminder that keys take the form `-`, so an agent can correct itself without the call failing. ## Workspace The backend the server resolved, and how it is configured.
workspace\_info() Source
Reports which backend the server resolved. On Modal it also reports the workspace and environment calls go to, how many apps are deployed, and whether Modal credentials are present. Takes no parameters.
## Discover Finding a tool in the catalog.
list\_tools() Source
Lists the available tools. On Modal this defaults to the tools deployed in the workspace; on `local` every registered tool is available. Restrict to tools actually deployed in this workspace. Pass `false` to see the full catalog, including tools that would have to be deployed first.
search\_tools() Source
Finds tools by keyword, matching against the tool key and its description. The keyword to match. Restrict to deployed tools, as in `list_tools`.
## Inspect A tool's typed contract: its schemas, an example input, and its citation.
get\_tool\_schema() Source
Returns the input, config, and output schemas for a tool. Arguments are validated strictly against them, and unknown fields are rejected. The tool to describe.
get\_tool\_example() Source
Returns a known-good example input for a tool, or null when the tool declares none. Bulky values such as structure coordinates are elided, so the result shows the shape rather than a runnable payload. The tool to fetch an example for.
get\_tool\_citation() Source
Returns the BibTeX citation and DOI for the method a tool implements. The tool to fetch a citation for.
## Run Executing a tool and returning its result.
run\_tool() Source
Runs a tool and blocks until it finishes. Most tools return in seconds once warm; the first call after a few minutes idle pays a container start and a model load, and some tools, such as binder design and diffusion, run for many minutes. The tool to run. The tool's input model. Validated strictly against its schema. The tool's config model. Directory large output fields are written into. Run the tool's canonical example input without supplying it. Override the server's backend for this call alone — `"local"`, `"modal"`, or `"proto"`. Omit it to use the backend the server was started with.
## Deploy Provisioning a tool on Modal. Not registered on the local backend, which has nothing to deploy.
deploy\_tool() Source
Deploys the Modal app serving a tool. The deployment builds a container image and then executes the tool once, on a GPU where the tool requires one. Both are billed to your own Modal account, and both occur before any result is returned. The operation may take several minutes, and progress is reported as the build advances through its phases. The tool to deploy. The target Modal environment. Required rather than inherited, so an accidental deployment to production is not possible.
You are asked to confirm before anything is built. Declining deploys nothing and incurs no cost. A client that cannot present the prompt is treated as a refusal. ## Next Steps Install the extra, register the server, and select a backend. How the server uses Modal, and the confirmation step behind `deploy_tool`. The catalog these tools operate over, with per-tool reference pages. The same Input plus Config to Output contract, from Python.