title: Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures.
abstract: BACKGROUND
  Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting complex structures is critical to reveal molecular mechanisms by which proteins operate. Despite recent advances in the development of new methods to model macromolecular assemblies, most current methodologies are designed to work with experimentally determined protein structures. However, because only computer-generated models are available for a large number of proteins in a given genome, computational tools should tolerate structural inaccuracies in order to perform the genome-wide modeling of PPIs.
  
  
  RESULTS
  To address this problem, we developed eRank(PPI), an algorithm for the identification of near-native conformations generated by protein docking using experimental structures as well as protein models. The scoring function implemented in eRank(PPI) employs multiple features including interface probability estimates calculated by eFindSite(PPI) and a novel contact-based symmetry score. In comparative benchmarks using representative datasets of homo- and hetero-complexes, we show that eRank(PPI) consistently outperforms state-of-the-art algorithms improving the success rate by ~10 %.
  
  
  CONCLUSIONS
  eRank(PPI) was designed to bridge the gap between the volume of sequence data, the evidence of binary interactions, and the atomic details of pharmacologically relevant protein complexes. Tolerating structure imperfections in computer-generated models opens up a possibility to conduct the exhaustive structure-based reconstruction of PPI networks across proteomes. The methods and datasets used in this study are available at www.brylinski.org/erankppi.
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. smahes2@tigers.lsu.edu.
authors.forename: Surabhi
authors.initials: S
authors.lastname: Maheshwari
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. michal@brylinski.org.|Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, 70803, USA. michal@brylinski.org.
authors.forename: Michal
authors.initials: M
authors.lastname: Brylinski
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D062105:Molecular Docking Simulation / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D000069553:Supervised Machine Learning; D013816:Thermodynamics
chemical_list: D011506:Proteins