title: Protein-protein binding site identification by enumerating the configurations.
abstract: BACKGROUND
  The ability to predict protein-protein binding sites has a wide range of applications, including signal transduction studies, de novo drug design, structure identification and comparison of functional sites. The interface in a complex involves two structurally matched protein subunits, and the binding sites can be predicted by identifying structural matches at protein surfaces.
  
  
  RESULTS
  We propose a method which enumerates "all" the configurations (or poses) between two proteins (3D coordinates of the two subunits in a complex) and evaluates each configuration by the interaction between its components using the Atomic Contact Energy function. The enumeration is achieved efficiently by exploring a set of rigid transformations. Our approach incorporates a surface identification technique and a method for avoiding clashes of two subunits when computing rigid transformations. When the optimal transformations according to the Atomic Contact Energy function are identified, the corresponding binding sites are given as predictions. Our results show that this approach consistently performs better than other methods in binding site identification.
  
  
  CONCLUSIONS
  Our method achieved a success rate higher than other methods, with the prediction quality improved in terms of both accuracy and coverage. Moreover, our method is being able to predict the configurations of two binding proteins, where most of other methods predict only the binding sites. The software package is available at http://sites.google.com/site/guofeics/dobi for non-commercial use.
authors: Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.
authors: Fei
authors: F
authors: Guo
authors: Shuai Cheng
authors: SC
authors: Li
authors: Lusheng
authors: L
authors: Wang
authors: Daming
authors: D
authors: Zhu
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D012984:Software
chemical_list: D046912:Multiprotein Complexes