Identify and analyze transport tunnels in protein structures from PDB inputs.
npx skills add https://github.com/LiorZ/protein-design-skills --skill caver
Please help me install this Agent Skill. Skill: caver Source: https://github.com/LiorZ/protein-design-skills/tree/main/skills/caver Command: npx skills add https://github.com/LiorZ/protein-design-skills --skill caver
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.
Run the CAVER SIF on your input PDB/MD ensemble to discover tunnels, generate cluster reports, and create visualization assets.
High-intent search queries and answers about installing and using this skill.
Identify and analyze transport tunnels in protein structures by running the CAVER SIF on PDB inputs or MD ensembles. The process locates tunnels, clusters them across frames, ranks clusters by throughput, and reports bottlenecks, lengths, radii, and curvature.
Visualize protein transport tunnels using the generated PyMOL and VMD visualization scripts emitted as outputs. These scripts render the tunnel meshes and bottleneck geometries calculated from your PDB or MD ensemble inputs.
Analyze substrate pathways in MD ensembles by clustering tunnels across frames. The analysis ranks clusters by throughput to identify the most viable transport pathways and bottleneck geometries within your molecular dynamics trajectory.
Tunnel analysis requires a CAVER SIF image, PDB inputs or an MD ensemble, and a configuration file. You must also specify a starting point using atoms, residues, or coordinates to map the buried active site pathways.
Cluster and rank protein tunnels by throughput using containerized CAVER execution. The analysis groups tunnels across trajectory frames, evaluates bottleneck radii and curvature, and generates CSV summary reports.
Tunnel analysis supports downstream integration with protein design workflows. It emits CSV data outputs, mesh files, and visualization scripts that map substrate pathways for tunnel engineering and design insights.
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