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Install in OpenClaw
/install pharmaclaw-alphafold-agent
Description
Compliant AlphaFold Agent for protein structure retrieval, ESMFold prediction, binding site detection, and RDKit ligand docking. Fetches public PDB/AlphaFold...
Usage Guidance
This skill appears to do what it says and does not request credentials or hidden endpoints, but treat it as a proof-of-concept/demo: ESMFold prediction is mocked, binding-site detection and docking are simplistic, and the script contains runtime bugs (missing Draw import, minimal error handling). If you plan to use it in production, review and fix the code, add input validation and HTTP/response checks, replace mocks with real ESMFold/fpocket/Vina components, and run it in an isolated/sandbox environment. As with any third-party script from an unknown source, inspect the code and test on non-sensitive systems before trusting it with important data.
Capability Analysis
Type: OpenClaw Skill
Name: pharmaclaw-alphafold-agent
Version: 1.0.0
The skill bundle is a legitimate tool for protein structure retrieval and molecular docking. The script `scripts/alphafold_agent.py` interacts with public scientific databases (RCSB PDB) and uses standard bioinformatics libraries (RDKit, Biopython) as described in `SKILL.md`. While some functions are currently mocks and there is a minor missing import for visualization, there is no evidence of malicious intent, data exfiltration, or unauthorized execution.
Capability Assessment
Purpose & Capability
The name/description (structure retrieval, ESMFold prediction, binding site detection, RDKit docking) matches the code and dependencies (requests, biopython, RDKit). However ESMFold prediction is explicitly mocked in the script (predict_esmfold writes a placeholder PDB) rather than invoking HuggingFace/ESMFold; docking and pocket detection are simplified/mocked. This is coherent for a demo but not a full production implementation.
Instruction Scope
SKILL.md and the script instruct the agent to fetch public PDBs (RCSB), optionally read a FASTA file, run a local mock prediction, detect pockets and run an RDKit-based docking/emedding. The script writes files locally and performs HTTP requests only to legitimate public endpoints (RCSB and AlphaFold EBI). It does not read or exfiltrate unrelated system files or request credentials.
Install Mechanism
No install spec is provided (instruction-only skill with one included script). That lowers installation risk; packages listed (rdkit-pypi, biopython, requests) are consistent with functionality. No arbitrary downloads or extract/install steps are present.
Credentials
The skill declares no required environment variables, no credentials, and requests no config paths. The runtime code also does not read environment variables or secrets.
Persistence & Privilege
always is false and the skill does not request persistent presence or modify other skills or system-wide settings. It runs as a one-off script that reads/writes local files.
How to Use
- Make sure OpenClaw is installed (local or Docker)
- Run the install command in chat:
/install pharmaclaw-alphafold-agent - After installation, invoke the skill by name or use
/pharmaclaw-alphafold-agent - Provide required inputs per the skill's parameter spec and get structured output
Version History
v1.0.0
pharmaclaw-alphafold-agent v1.0.0
- Initial release of a compliant AlphaFold agent for protein structure retrieval, ESMFold prediction, binding pocket detection, and basic RDKit ligand docking.
- Supports fetching public PDB/AlphaFold DB structures, predicting 3D folds, detecting pockets, and docking ligands using SMILES input.
- Integrates into multi-step pipelines with clear input/output JSON formats and chain connectivity.
- Operates fully on open-source/commercially permissible resources; does not require proprietary servers.
- Includes limitations for docking (RDKit scoring) and binding site detection refinement.
Metadata
Frequently Asked Questions
What is Pharmaclaw Alphafold Agent?
Compliant AlphaFold Agent for protein structure retrieval, ESMFold prediction, binding site detection, and RDKit ligand docking. Fetches public PDB/AlphaFold... It is an AI Agent Skill for Claude Code / OpenClaw, with 351 downloads so far.
How do I install Pharmaclaw Alphafold Agent?
Run "/install pharmaclaw-alphafold-agent" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.
Is Pharmaclaw Alphafold Agent free?
Yes, Pharmaclaw Alphafold Agent is completely free, licensed under MIT-0. You can download, install and use it at no cost.
Which platforms does Pharmaclaw Alphafold Agent support?
Pharmaclaw Alphafold Agent is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).
Who created Pharmaclaw Alphafold Agent?
It is built and maintained by Cheminem (@cheminem); the current version is v1.0.0.
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