caver
CommunityIdentify and visualize protein tunnels with CAVER
AuthorLiorZ
Version1.0.0
Installs0
System Documentation
What problem does it solve?
The CAVER skill identifies and analyzes transport tunnels in protein structures to map how substrates could traverse from buried active sites to the surface, enabling tunnel engineering and design insights.
Core Features & Use Cases
- Detects tunnels in static PDBs or MD ensembles and reports bottlenecks, lengths, radii, and curvature.
- Clusters tunnels across frames, ranks clusters by throughput, and generates ready-to-visualize outputs (summary, analysis, data, PyMOL/VMD scripts).
- Supports starting-point specification (atoms, residues, or coordinates), containerized execution via Apptainer/SIF, and downstream integration with design workflows.
Quick Start
Run the CAVER SIF on your input PDB/MD ensemble to discover tunnels, generate cluster reports, and create visualization assets.
Dependency Matrix
Required Modules
None requiredComponents
references
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: caver Download link: https://github.com/LiorZ/protein-design-skills/archive/main.zip#caver Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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