Xpersona
agentCLAWHUBUnverified

Protein Design

Protein, peptide, antibody, nanobody, binder, enzyme, and sequence design workflows using Boltzgen, RFdiffusion, RFdiffusion2, RFdiffusion3, ProteinMPNN, Lig...

OpenClaw
View on ClawHubHomepage

Rank

62

Safety

84

Downloads

1.5k

Updated

Oct 10, 2026

Version

1.0.8

Source

CLAWHUB

About

What it does, and when to use it.

Capability contract not published. No trust telemetry is available yet. 1.5K downloads reported by the source. Last updated 10/10/2026.

Avoid when

  • Contract metadata is missing or unavailable for deterministic execution.

Risk flags: missing_or_unavailable_contract, trust_data_unavailable, schema_references_missing

Public facts

Every fact links back to the source it came from.

Vendor
Clawhubvendor · observed Oct 10, 2026
Protocol compatibility
OpenClawcompatibility · observed Oct 10, 2026
Adoption signal
1.5K downloadsadoption · observed Oct 10, 2026
Latest release
1.0.8release · observed May 31, 2026
Handshake status
UNKNOWNsecurity

Install and run

Setup complexity: low.

clawhub skill install s170qp1q4twz35wa85ppa8894h83w461:protein-design
  1. Install using `clawhub skill install s170qp1q4twz35wa85ppa8894h83w461:protein-design` in an isolated environment before connecting it to live workloads.
  2. No published capability contract is available yet, so validate auth and request/response behavior manually.
  3. Review the upstream CLAWHUB listing at https://clawhub.ai/sciminer/protein-design before using production credentials.

Contract: missing

curl -s "https://www.xpersona.co/api/v1/agents/clawhub-sciminer-protein-design/snapshot"

Documentation

CLAWHUB

65,414 characters of source documentation, loaded on request.

Extracted files

3 files captured from the source.

SKILL.md

---
name: protein-design
description: Protein, peptide, antibody, nanobody, binder, enzyme, and sequence design workflows using Boltzgen, RFdiffusion, RFdiffusion2, RFdiffusion3, ProteinMPNN, LigandMPNN, and BindCraft through SciMiner APIs.
credential_files:
    - ~/.config/sciminer/credentials.json
---

# Protein Design Skill

This skill covers de novo and constrained protein design workflows using:

- `Boltzgen`
- `RFdiffusion`
- `RFdiffusion2`
- `RFdiffusion3`
- `ProteinMPNN`
- `LigandMPNN`
- `BindCraft`
- `FreeBindCraft` when the user requests the open-source BindCraft variant

## When to use this skill

- Design proteins, peptides, antibodies, or nanobodies to bind a target antigen
    or small molecule
- Generate protein backbones from scratch, from motifs, or under symmetry,
    hotspot, contig, or partial-redesign constraints
- Scaffold catalytic motifs or design enzyme active sites around ligands
- Design protein binders against protein, DNA, or small-molecule targets
- Redesign amino-acid sequences for a fixed protein backbone or complex
- Run an end-to-end binder-design pipeline that includes structure prediction,
    sequence optimization, and filtering

## 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 `provider_name`, `tool_name`, allowed
`parameters`, file-upload behavior, request encoding, and the example
submission flow for this skill's included tools.

Use these SciMiner Markdown docs:

- `Boltzgen` -> `Boltzgen_api_doc.md`
- `RFdiffusion` -> `RFdiffusion_api_doc.md`
- `RFdiffusion2` -> `RFdiffusion2_api_doc.md`
- `RFdiffusion3` -> `RFdiffusion3_api_doc.md`
- `ProteinMPNN` -> `ProteinMPNN_api_doc.md`
- `LigandMPNN` -> `LigandMPNN_api_doc.md`
- `BindCraft` -> `BindCraft_api_doc.md`
- `FreeBindCraft` -> `FreeBindCraft_api_doc.md`

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

_meta.json

{
  "ownerId": "kn725br751g8y5tkj1h6d2krf58356et",
  "slug": "protein-design",
  "version": "1.0.8",
  "publishedAt": 1780221445485
}

skill-card.md

## Description:

Protein, peptide, antibody, nanobody, binder, enzyme, and sequence design workflows using Boltzgen, RFdiffusion, RFdiffusion2, RFdiffusion3, ProteinMPNN, LigandMPNN, and BindCraft through SciMiner APIs.

This skill is ready for commercial/non-commercial use.

## Publisher:

[sciminer](https://clawhub.ai/user/sciminer)

### License/Terms of Use:

MIT-0

## Use Case:

Developers, researchers, and external users use this skill to run SciMiner protein-design workflows for backbone generation, binder design, antibody or nanobody design, enzyme scaffolding, sequence redesign, and multi-step design pipelines.

### Deployment Geography for Use:

Global

## Known Risks and Mitigations:

Risk: Mutable online SciMiner documentation can change authenticated request behavior.

Mitigation: Review the selected SciMiner Markdown document before each invocation and use the skill only when the documentation host is trusted.

Risk: Protein structures, sequences, and design constraints may be sent through SciMiner workflows.

Mitigation: Avoid sensitive or unpublished data unless approved, and verify upload destinations before submitting files.

Risk: The skill requires a SciMiner API key.

Mitigation: Use a dedicated, revocable key stored outside the repository and do not print, persist, or log the key.

## Reference(s):

- [SciMiner Tool API Documentation](https://sciminer.tech/tool_api_files/)
- [SciMiner API Key Utility](https://sciminer.tech/utility)
- [ClawHub Protein Design Skill](https://clawhub.ai/sciminer/skills/protein-design)

## Skill Output:

**Output Type(s):** [Guidance, Markdown, Code, Shell commands, Configuration instructions, API Calls]

**Output Format:** [Markdown summaries with JSON task results and SciMiner share URLs]

**Output Parameters:** [1D]

**Other Properties Related to Output:** [Uses selected SciMiner Markdown docs as the payload source and returns task share URLs for completed or long-running jobs.]

## Skill Version(s):

1.0.8 (source: server release metadata)

## Ethical Considerations:

Users should evaluate whether this skill is appropriate for their environment, review any generated or modified files before relying on them, and apply their organization's safety, security, and compliance requirements before deployment.

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Machine-readable data

The same record, as JSON, for agents and crawlers.

{
  "facts": [
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      "category": "vendor",
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      "sourceType": "profile",
      "confidence": "medium",
      "observedAt": "2026-10-10T11:34:16.367Z",
      "isPublic": true
    },
    {
      "factKey": "protocols",
      "category": "compatibility",
      "label": "Protocol compatibility",
      "value": "OpenClaw",
      "href": "https://www.xpersona.co/api/v1/agents/clawhub-sciminer-protein-design/contract",
      "sourceUrl": "https://www.xpersona.co/api/v1/agents/clawhub-sciminer-protein-design/contract",
      "sourceType": "contract",
      "confidence": "medium",
      "observedAt": "2026-10-10T11:34:16.367Z",
      "isPublic": true
    },
    {
      "factKey": "traction",
      "category": "adoption",
      "label": "Adoption signal",
      "value": "1.5K downloads",
      "href": "https://clawhub.ai/sciminer/protein-design",
      "sourceUrl": "https://clawhub.ai/sciminer/protein-design",
      "sourceType": "profile",
      "confidence": "medium",
      "observedAt": "2026-10-10T11:34:16.367Z",
      "isPublic": true
    },
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      "factKey": "latest_release",
      "category": "release",
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      "sourceUrl": "https://clawhub.ai/sciminer/protein-design",
      "sourceType": "release",
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      "isPublic": true
    },
    {
      "factKey": "handshake_status",
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      "label": "Handshake status",
      "value": "UNKNOWN",
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      "sourceUrl": "https://www.xpersona.co/api/v1/agents/clawhub-sciminer-protein-design/trust",
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  "events": [
    {
      "eventType": "release",
      "title": "Release 1.0.8",
      "description": "**Expanded to cover multiple state-of-the-art protein design APIs and workflows alongside Boltzgen.** - Now supports Boltzgen, RFdiffusion, RFdiffusion2, RFdiffusion3, ProteinMPNN, LigandMPNN, BindCraft, and FreeBindCraft tools via SciMiner. - Replaces the local registry with live doc-based parameter and API resolution from authoritative Markdown files at https://sciminer.tech/tool_api_files/. - Handles de novo backbone generation, binder design, antibody/nanobody design, enzyme and catalytic motif scaffolding, sequence design, and end-to-end pipeline workflows. - Ensures parameter names, payloads, file upload forms, and allowed values always match the referenced online tool doc, not agent memory. - Guides users to the most appropriate tool or tool sequence for their design goals, including multi-step workflows. - Users continue to supply their SciMiner API key as before; all invocations and summaries now cite the selected API doc rather than a local script/registry.",
      "href": "https://clawhub.ai/sciminer/protein-design",
      "sourceUrl": "https://clawhub.ai/sciminer/protein-design",
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      "observedAt": "2026-05-31T09:57:25.485Z",
      "isPublic": true
    }
  ]
}

Record generated Oct 10, 2026.

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