title: Large-scale comparison of four binding site detection algorithms.
abstract: A large-scale evaluation and comparison of four cavity detection algorithms was carried out. The algorithms SiteFinder, fpocket, PocketFinder, and SiteMap were evaluated on a protein test set containing 5416 protein-ligand complexes and 9900 apo forms, corresponding to a subset of the set used earlier for benchmarking the PocketFinder algorithm. For the holo structures, all four algorithms correctly identified a similar amount of pockets (around 95%). SiteFinder, using optimized parameters, SiteMap, and fpocket showed similar pocket ranking performance, which was defined by ranking the correct binding site on rank 1 of the predictions or within the first 5 ranks of the predictions. On the apo structures, PocketFinder especially and also SiteFinder (optimized parameters) performed best, identifying 96% and 84% of all binding sites, respectively. The fpocket program predicts binding sites most accurately among the algorithms evaluated here. SiteFinder needed an average calculation time of 1.6 s compared with 2 min for SiteMap and around 2 s for fpocket.
authors.affiliation: Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France.
authors.forename: Peter
authors.initials: P
authors.lastname: Schmidtke
authors.forename: Catherine
authors.initials: C
authors.lastname: Souaille
authors.forename: Frédéric
authors.initials: F
authors.lastname: Estienne
authors.forename: Nicolas
authors.initials: N
authors.lastname: Baurin
authors.forename: Romano T
authors.initials: RT
authors.lastname: Kroemer
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D008024:Ligands; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins