domains / families / science / binding-site-detection

binding-site-detection

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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.

When to use

• detecting cavities on an apo structure with no bound ligand
• choosing geometric pocket enumeration vs ML ligandability scoring
• detecting cryptic or transient pockets over an MD or conformational ensemble
• detecting on a predicted model
• ranking pockets by druggability or ligandability score

When not to use

• mapping residues around a bound ligand in a holo structure
• interface-analysis

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