Detects putative ligand-binding pockets and druggable cavities de novo on an apo protein structure with fpocket, P2Rank, CASTp, and DoGSiteScorer, ranking them by druggability/ligandability score. Use when detecting cavities on an apo structure with no bound ligand; choosing geometric pocket enumeration (fpocket alpha-spheres, CASTp) vs ML ligandability scoring (P2Rank, DoGSiteScorer); recognizing that a geometric cavity is a hypothesis, not automatically a functional or druggable site (may be a crystal-additive or non-functional cleft); knowing druggability scores were trained on holo sets and under-detect apo, shallow, and cryptic pockets; detecting cryptic or transient pockets over an MD or conformational ensemble (mdpocket); and detecting on a predicted model whose pocket-lining rotamers are the least reliable atoms. Keywords binding site, pocket, cavity, druggability, ligandability, fpocket, P2Rank, CASTp, DoGSiteScorer, apo, cryptic pocket, alpha sphere, mdpocket.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryScience & researchStars0
About this skill
Detects putative ligand-binding pockets and druggable cavities de novo on an apo protein structure with fpocket, P2Rank, CASTp, and DoGSiteScorer, ranking them by druggability/ligandability score. Use when detecting cavities on an apo structure with no bound ligand; choosing geometric pocket enumeration (fpocket alpha-spheres, CASTp) vs ML ligandability scoring (P2Rank, DoGSiteScorer); recognizing that a geometric cavity is a hypothesis, not automatically a functional or druggable site (may be a crystal-additive or non-functional cleft); knowing druggability scores were trained on holo sets and under-detect apo, shallow, and cryptic pockets; detecting cryptic or transient pockets over an MD or conformational ensemble (mdpocket); and detecting on a predicted model whose pocket-lining rotamers are the least reliable atoms. Keywords binding site, pocket, cavity, druggability, ligandability, fpocket, P2Rank, CASTp, DoGSiteScorer, apo, cryptic pocket, alpha sphere, mdpocket.
Quick start
Copy the install prompt. Use the green button above this README.
Send it to your agent. Paste it into your coding agent’s chat and send.
Review the setup. Your agent checks the skill’s instructions, requirements, and installation scope.
Detects putative ligand-binding pockets and druggable cavities de novo on an apo protein structure with fpocket, P2Rank, CASTp, and DoGSiteScorer, ranking them by druggability/ligandability score. Use when detecting cavities on an apo structure with no bound ligand; choosing geometric pocket enumeration (fpocket alpha-spheres, CASTp) vs ML ligandability scoring (P2Rank, DoGSiteScorer); recognizing that a geometric cavity is a hypothesis, not automatically a functional or druggable site (may be a crystal-additive or non-functional cleft); knowing druggability scores were trained on holo sets and under-detect apo, shallow, and cryptic pockets; detecting cryptic or transient pockets over an MD or conformational ensemble (mdpocket); and detecting on a predicted model whose pocket-lining rotamers are the least reliable atoms. Keywords binding site, pocket, cavity, druggability, ligandability, fpocket, P2Rank, CASTp, DoGSiteScorer, apo, cryptic pocket, alpha sphere, mdpocket.
About this listing
Category
Science & research
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI