title: Alignment of non-covalent interactions at protein-protein interfaces.
abstract: BACKGROUND
  The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces.
  
  
  RESULTS
  Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions.
  
  
  CONCLUSIONS
  The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.
authors.affiliation: Max-Planck-Institut für Informatik, Saarbrücken, Germany. hzhu@mpi-inf.mpg.de
authors.forename: Hongbo
authors.initials: H
authors.lastname: Zhu
authors.forename: Ingolf
authors.initials: I
authors.lastname: Sommer
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
authors.forename: Francisco S
authors.initials: FS
authors.lastname: Domingues
mesh_terms: D001665:Binding Sites; D001671:Biochemistry / Q000379:methods*; D015704:CD4 Antigens / Q000737:chemistry; D016000:Cluster Analysis; D030562:Databases, Protein; D015699:HIV Envelope Protein gp120 / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D007376:Interleukin-2 / Q000737:chemistry; D053645:Interleukin-2 Receptor alpha Subunit / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D025941:Protein Interaction Mapping; D015203:Reproducibility of Results
chemical_list: D015704:CD4 Antigens; D015699:HIV Envelope Protein gp120; D007376:Interleukin-2; D053645:Interleukin-2 Receptor alpha Subunit; C514793:gp120 protein, Human immunodeficiency virus 1