title: Prediction of protein-binding areas by small-world residue networks and application to docking.
abstract: BACKGROUND
  Protein-protein interactions are involved in most cellular processes, and their detailed physico-chemical and structural characterization is needed in order to understand their function at the molecular level. In-silico docking tools can complement experimental techniques, providing three-dimensional structural models of such interactions at atomic resolution. In several recent studies, protein structures have been modeled as networks (or graphs), where the nodes represent residues and the connecting edges their interactions. From such networks, it is possible to calculate different topology-based values for each of the nodes, and to identify protein regions with high centrality scores, which are known to positively correlate with key functional residues, hot spots, and protein-protein interfaces.
  
  
  RESULTS
  Here we show that this correlation can be efficiently used for the scoring of rigid-body docking poses. When integrated into the pyDock energy-based docking method, the new combined scoring function significantly improved the results of the individual components as shown on a standard docking benchmark. This improvement was particularly remarkable for specific protein complexes, depending on the shape, size, type, or flexibility of the proteins involved.
  
  
  CONCLUSIONS
  The network-based representation of protein structures can be used to identify protein-protein binding regions and to efficiently score docking poses, complementing energy-based approaches.
authors.affiliation: Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center, Barcelona 08034, Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Pons
authors.forename: Fabian
authors.initials: F
authors.lastname: Glaser
authors.forename: Juan
authors.initials: J
authors.lastname: Fernandez-Recio
mesh_terms: D000465:Algorithms; D006801:Humans; D008958:Models, Molecular; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D013816:Thermodynamics
chemical_list: D011506:Proteins