binding-site-analysis
Decide whether a protein has a pocket worth targeting, and where it is, before committing to a docking or design campaign. Use this skill to run fpocket cavity detection, rank cavities by druggability and volume, compare apo and holo conformations to spot induced fit, identify allosteric and cryptic cavities that only open in simulation, and convert a chosen cavity into the search box coordinates a docking run needs. Also trigger on fpocket, cavity detection, druggability score, alpha sphere, cryptic pocket, allosteric site, pocket volume, hotspot mapping, or undruggable target assessment.
- Version
- 1.0
- License
- MIT
- Compatibility
- Requires Python 3.10+. The bundled scripts parse fpocket output and emit box coordinates using only the standard library. Detecting cavities needs the fpocket binary (conda-forge or apt, MIT) on PATH. Cryptic-cavity workflows additionally need a molecular dynamics engine; no GPU is required for static detection.
Pinned to revision f67572246d9b, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
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- Bash
Files
- skills/binding-site-analysis/SKILL.md
- skills/binding-site-analysis/references/cryptic-and-allosteric.md
- skills/binding-site-analysis/references/druggability.md
- skills/binding-site-analysis/references/fpocket-output.md
- skills/binding-site-analysis/scripts/pocket_box.py
- skills/binding-site-analysis/scripts/pocket_report.py
- skills/binding-site-analysis/scripts/site_compare.py
Every link opens the file at its source, pinned to the revision this page describes.