title: An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites.
abstract: Accurate alignment of protein-protein binding sites can aid in protein docking studies and constructing templates for predicting structure of protein complexes, along with in-depth understanding of evolutionary and functional relationships. However, over the past three decades, structural alignment algorithms have focused predominantly on global alignments with little effort on the alignment of local interfaces. In this paper, we introduce the PBSalign (Protein-protein Binding Site alignment) method, which integrates techniques in graph theory, 3D localized shape analysis, geometric scoring, and utilization of physicochemical and geometrical properties. Computational results demonstrate that PBSalign is capable of identifying similar homologous and analogous binding sites accurately and performing alignments with better geometric match measures than existing protein-protein interface comparison tools. The proportion of better alignment quality generated by PBSalign is 46, 56, and 70 percent more than iAlign as judged by the average match index (MI), similarity index (SI), and structural alignment score (SAS), respectively. PBSalign provides the life science community an efficient and accurate solution to binding-site alignment while striking the balance between topological details and computational complexity.
authors.forename: Bin
authors.initials: B
authors.lastname: Pang
authors.forename: David
authors.initials: D
authors.lastname: Schlessman
authors.forename: Xingyan
authors.initials: X
authors.lastname: Kuang
authors.forename: Nan
authors.initials: N
authors.lastname: Zhao
authors.forename: Daniel
authors.initials: D
authors.lastname: Shyu
authors.forename: Dmitry
authors.initials: D
authors.lastname: Korkin
authors.forename: Chi-Ren
authors.initials: CR
authors.lastname: Shyu
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins