Large-Scale Comparison of Four Binding Site Detection Algorithms
Citations Over TimeTop 10% of 2010 papers
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.
Related Papers
- → Remarks on Algorithm 2, Algorithm 3, Algorithm 15, Algorithm 25 and Algorithm 26(1961)2 cited
- → Remarks on Algorithm 332: Jacobi polynomials: Algorithm 344: student's t -distribution: Algorithm 351: modified Romberg quadrature: Algorithm 359: factoral analysis of variance(1970)
- Using DataGrid Control to Realize DataBase of Querying in VB6.0(2000)
- Susquehanna Chorale Spring Concert "Roots and Wings"(2017)
- → ИСПОЛЬЗОВAНИЕ ПОТЕНЦИAЛA СОЦИAЛЬНЫХ ПAРТНЕРОВ В ПОДГОТОВКЕ БУДУЩИХ ПЕДAГОГОВ(2024)