CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

• DOI: 10.1021/ci200082t
• Publication Date: 2011-07-05T16:22:29Z
• Authors: James B. Dunbar; Richard D. Smith; Chao-Yie Yang; Peter Man-Un Ung; Katrina W. Lexa; Nickolay A. Khazanov; Jeanne A. Stuckey; Shaomeng Wang; Heather A. Carlson
• Keywords: Docking (animal); Protein Data Bank; Data set; Benchmark (surveying); Training set

A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) aims to collect available data from industry academia which may be used this purpose (www.csardock.org). Also, CSAR charged with organizing community-wide exercises based on collected data. first these was aimed gauge overall state scoring, using a large diverse set protein–ligand complexes. Participants were asked calculate affinity complexes as provided then recalculate changes improve their specific method. This selected existing PDB entries had binding (Kd or Ki) Binding MOAD, augmented PDBbind. final contains 343 spans 14 pKd. Sixteen proteins have three more set, user could start an inspection congeneric series. Inherent experimental error limits possible correlation between scores measured affinity; R2 limited ∼0.9 when fitting without over parametrizing. ∼0.8 scoring method trained outside details how initially selected, process by it matured better fit needs community are presented. Many groups generously participated improving underscores value supportive, collaborative effort moving our field forward.