How do I install the Protein Structure skill?

Run npx skillmds add vimalinx/protein-structure in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Protein Structure safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Protein Structure?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Protein Structure free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Protein Structure?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Protein Structure by vimalinx — Agent Skill

Name: Protein Structure
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

protein-structure

Workspace-level gateway for structure-oriented work. In this repo, the strongest local assets are the checked-out RFdiffusion and evo2 repositories plus Docker, not a ready-to-run AlphaFold/ColabFold desktop stack.

Quick Start

Available local assets: /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion, /home/vimalinx/Projects/bio_studio/repositories/active/evo2, /usr/bin/docker
Fast availability check: command -v colabfold_batch pymol chimera chimerax foldseek mmseqs fpocket
Current practical path: use repo-backed Docker workflows rather than assuming local GUI prediction tools exist

When To Use This Tool

Deciding how to approach a protein-structure task in this workspace
Routing between structure design (RFdiffusion) and sequence-model analysis (evo2)
Auditing whether local structure-prediction tools are actually installed before planning around them
Staging follow-on structure workflows once prerequisites are satisfied

Common Patterns

# Check which structure tools are really installed
command -v colabfold_batch pymol chimera chimerax foldseek mmseqs fpocket

# Use the local RFdiffusion repo for generative design
cd /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion
./test_rfdiffusion.sh

# Inspect the local Evo 2 repo for sequence-model-based analysis
cd /home/vimalinx/Projects/bio_studio/repositories/active/evo2
python examples/run_evo2.py

Recommended Workflow

Verify the required predictor or viewer is actually present before promising a structure workflow.
If you need generative backbone or binder design, start from the local RFdiffusion repo.
If you need sequence-model scoring or embeddings on DNA-scale inputs, evaluate whether Evo 2 is the right supporting asset.
Install missing prediction/visualization tools explicitly before planning around ColabFold, PyMOL, or Chimera-based steps.

Guardrails

colabfold_batch, pymol, chimera, chimerax, foldseek, mmseqs, and fpocket are not currently on PATH in this workspace.
RFdiffusion is present locally, but its Docker image is not prebuilt yet.
The local Evo 2 repo exists, but direct import evo2 currently fails because vortex is missing.
Do not present RFdiffusion as a native fold-prediction replacement; it is primarily a generative structure-design workflow.

---name: protein-structuredescription: Use when planning or staging protein-structure prediction or structure-design work in this workspace, especially when deciding between missing local predictors and the repos that are actually present.--- # protein-structure Workspace-level gateway for structure-oriented work. In this repo, the strongest local assets are the checked-out `RFdiffusion` and `evo2` repositories plus Docker, not a ready-to-run AlphaFold/ColabFold desktop stack. ## Quick Start - **Available local assets:** `/home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion`, `/home/vimalinx/Projects/bio_studio/repositories/active/evo2`, `/usr/bin/docker` - **Fast availability check:** `command -v colabfold_batch pymol chimera chimerax foldseek mmseqs fpocket` - **Current practical path:** use repo-backed Docker workflows rather than assuming local GUI prediction tools exist ## When To Use This Tool - Deciding how to approach a protein-structure task in this workspace - Routing between structure design (`RFdiffusion`) and sequence-model analysis (`evo2`) - Auditing whether local structure-prediction tools are actually installed before planning around them - Staging follow-on structure workflows once prerequisites are satisfied ## Common Patterns ```bash # Check which structure tools are really installed command -v colabfold_batch pymol chimera chimerax foldseek mmseqs fpocket ``` ```bash # Use the local RFdiffusion repo for generative design cd /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion ./test_rfdiffusion.sh ``` ```bash # Inspect the local Evo 2 repo for sequence-model-based analysis cd /home/vimalinx/Projects/bio_studio/repositories/active/evo2 python examples/run_evo2.py ``` ## Recommended Workflow 1. Verify the required predictor or viewer is actually present before promising a structure workflow. 2. If you need generative backbone or binder design, start from the local `RFdiffusion` repo. 3. If you need sequence-model scoring or embeddings on DNA-scale inputs, evaluate whether Evo 2 is the right supporting asset. 4. Install missing prediction/visualization tools explicitly before planning around ColabFold, PyMOL, or Chimera-based steps. ## Guardrails - `colabfold_batch`, `pymol`, `chimera`, `chimerax`, `foldseek`, `mmseqs`, and `fpocket` are not currently on `PATH` in this workspace. - `RFdiffusion` is present locally, but its Docker image is not prebuilt yet. - The local Evo 2 repo exists, but direct `import evo2` currently fails because `vortex` is missing. - Do not present RFdiffusion as a native fold-prediction replacement; it is primarily a generative structure-design workflow.

Frequently asked questions