B-P.27: Apo, Holo, and Everything in Between: What State Are AlphaFold Binding Pockets In?
AlphaFold DB models are widely used for ligand-binding analysis, but a practical question remains: do their binding pockets look more like ligand-free apo states, ligand-bound holo states, or something in between? We addressed this using AHoJ-DB, which links experimentally observed alternative pocket conformations for the same protein regions. From 464,869 query-pocket entries with AlphaFold classifications, after filtering for usable classifications and at least one apo comparator, we retained 237,922 pockets from 12,255 UniProt accessions. At first glance, AlphaFold pockets appeared more holo-like than apo-like, but this imbalance moved toward — and past — equilibrium once overlapping pockets were merged into unified binding sites. More importantly, experimental apo/holo evidence balance did not produce a hard switch between classes; instead, AlphaFold pockets shifted gradually along an apo-holo continuum with the holo-to-apo experimental evidence ratio. We then tested whether this local pocket state mattered in downstream analyses.
Three structurally independent binding-site predictors (P2Rank, fpocket, IF-SitePred) all detected holo-like pockets more successfully than apo-like ones (63% vs 47%, 63% vs 50% and 68% vs 46%), and molecular docking of cognate PDB ligands agreed (69% vs 49%); pockets undetected by all three predictors were twice as likely to be apo-like (28% vs 14%). Success also rose with the holo-to-apo evidence ratio.These results suggest that AlphaFold pockets are best interpreted as occupying a measurable structural spectrum, and that this local pocket state can help flag when ligand placement and pocket prediction are likely to be straightforward or require extra caution.
Co-authors: Radoslav Krivak, Jiri Vondrasek, Marian Novotny, Derrick Agwora, David Hoksza, Chloé Weiler
Contact Attendee
Warning: Attempt to read property "user_email" on string in /home/1276969.cloudwaysapps.com/ydbgzhdjeq/public_html/wp-content/plugins/my-conference-now/functions.php on line 2826