Molecular Docking

Molecular docking workflows across Gnina, AutoDock Vina, PackDock, SurfDock, and DiffDock through SciMiner, with Gnina as the default engine.

Molecular Docking Skill

This skill groups protein-ligand docking workflows, including:

• pocket-guided docking with Gnina (default)
• classical docking with AutoDock Vina
• flexible docking with PackDock
• surface-geometry-assisted docking with SurfDock
• diffusion-model docking with DiffDock
• predicted binding-site detection with fpocket
• side-by-side comparison across multiple docking engines

When to use this skill

• Dock one or more ligands into a known or user-provided protein pocket
• Run a fast default docking workflow without manually choosing an engine
• Compare docking outcomes across multiple engines for robustness checks
• Use method-specific engines when the user explicitly requests one by name

Method selection rule

Docking engines:

• Default to Gnina for generic docking requests.
• Use the named engine when the user explicitly names one of Gnina, AutoDock Vina, PackDock, SurfDock, or DiffDock.
• Use PackDock for flexible (side-chain repacking) docking.
• Use SurfDock when surface-geometry awareness is requested or the pocket is shallow/cryptic.
• Gnina -> Gnina_api_doc.md
• AutoDock Vina -> AutoDock Vina_api_doc.md
• PackDock -> PackDock_api_doc.md
• Generic docking requests -> Gnina
• Requests that explicitly name an engine -> the named provider: AutoDock Vina, PackDock, SurfDock, or DiffDock
• Binding-pocket prediction before docking -> fpocket
• Multi-engine comparison or benchmarking -> run the requested provider set, using Gnina as the default when no engine is specified

Prerequisites

1. Obtain a free SciMiner API key from https://sciminer.tech/utility.
2. Store it outside this repository at ~/.config/sciminer/credentials.json with JSON shaped as {"api_key":"your_api_key_here"}.
3. For SciMiner calls, read the API key from ~/.config/sciminer/credentials.json and send it as the X-Auth-Token header.
4. Never print, persist, or store the API key in prompts, logs, or repository files. Agents should remember only the credential file path.

If ~/.config/sciminer/credentials.json is not available or does not contain an api_key field, stop and tell the user to obtain a free SciMiner API key from https://sciminer.tech/utility and store it in that file. Do not try to complete the task by switching to other tools or services.

Authoritative tool-doc source (required)

The published Markdown files under https://sciminer.tech/tool_api_files/ are the single source of truth for the selected docking tool's provider_name, tool_name, allowed parameters, file-upload behavior, request encoding, and submission flow.

The agent MUST:

1. Resolve the selected tool's Markdown file and read it before every invocation.
2. Never invent provider_name, tool_name, parameter names, enum values, upload-field names, content type, or submission flow from memory.
3. Extract and follow the selected doc section's exact:
   • Base URL
   • API endpoint
   • Content-Type
   • Authentication header
   • Tool Name
   • Method
   • Parameter table, including required fields and enum values
   • File-upload instructions and example code
4. Choose the correct section if the selected doc contains multiple tool variants, such as reference-ligand input vs pocket-center input.
5. Cite the selected Markdown doc as the payload source in summaries.

If a user-provided parameter is not present in the selected Markdown doc section, ask for correction or drop it with an explanation.

Required workflow

1. Determine which docking engine or engine set matches the user's request.
2. When no pocket input is available, run the supporting pocket-detection step first and then read the corresponding docking tool docs.
3. Read the selected tool Markdown file or files from https://sciminer.tech/tool_api_files/.
4. Choose the doc section that matches the user's input shape.
5. Collect any missing required parameters from the user.
6. Upload required file inputs exactly as described by the selected Markdown doc and replace local paths with returned file_id values.
7. Write or run the invocation code directly from the selected Markdown doc's base-information block, parameter table, file-upload instructions, and example code. Do not apply a shared invocation template or local registry abstraction in this skill.
8. Poll the task result and return the share_url in the final user-facing summary.

File upload rules

• Upload every required file parameter described by the selected Markdown doc before invocation.
• Replace local paths in parameters with the returned file_id strings.
• Use the upload form field documented by the selected Markdown doc.
• Skip optional file parameters that the user did not provide.

Expected result format

json

{
    "status": "SUCCESS",
    "result": {...},
    "task_id": "xxx",
    "share_url": "https://sciminer.tech/share?id=<task_id>&type=API_TOOL"
}

Workflow guidance

• Generic docking requests -> Gnina
• Requests that explicitly name an engine -> the named provider: AutoDock Vina, PackDock, SurfDock, or DiffDock
• Binding-pocket prediction before docking -> fpocket
• Multi-engine comparison or benchmarking -> run the requested provider set, using Gnina as the default when no engine is specified

Notes

• Use the selected Markdown doc under https://sciminer.tech/tool_api_files/ as the authoritative source for payload construction and invoke-method details.
• Read the SciMiner API key from ~/.config/sciminer/credentials.json and send it as the X-Auth-Token header. Do not print or persist the API key in prompts, logs, or repository files.
• If ~/.config/sciminer/credentials.json is missing or does not contain an api_key field, stop and tell the user to obtain a free SciMiner API key from https://sciminer.tech/utility and store it in that file.
• provider_name must exactly match the selected Markdown doc.
• Use the selected Markdown doc to determine file inputs, parameter placement, and any tool-specific submission details.
• Important: when summarizing results to users, attach the share_url links of every successful task at the end.
• For long-running tasks without a fixed ETA, poll for no more than 6000 seconds; if the task is still running, stop polling and return the current task_id and share_url so the user can check later.