title: SERAPhiC: a benchmark for in silico fragment-based drug design.
abstract: Our main objective was to compile a data set of high-quality protein-fragment complexes and make it publicly available. Once assembled, the data set was challenged using docking procedures to address the following questions: (i) Can molecular docking correctly reproduce the experimentally solved structures? (ii) How thorough must the sampling be to replicate the experimental data? (iii) Can commonly used scoring functions discriminate between the native pose and other energy minima? The data set, named SERAPhiC (Selected Fragment Protein Complexes), is publicly available in a ready-to-dock format ( http://www.iit.it/en/drug-discovery-and-development/seraphic.html ). It offers computational medicinal chemists a reliable test set for both in silico protocol assessment and software development.
authors.affiliation: Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy. angelo.favia@iit.it
authors.forename: Angelo D
authors.initials: AD
authors.lastname: Favia
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bottegoni
authors.forename: Irene
authors.initials: I
authors.lastname: Nobeli
authors.forename: Paola
authors.initials: P
authors.lastname: Bisignano
authors.forename: Andrea
authors.initials: A
authors.lastname: Cavalli
mesh_terms: D000465:Algorithms; D000818:Animals; D001419:Bacteria; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D030562:Databases, Protein; D055808:Drug Discovery / Q000379:methods*; D005658:Fungi; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D011506:Proteins; D012984:Software; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins