title: Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
abstract: Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.
authors.affiliation: Department of Physics, Chuo University, Bunkyo-ku, Tokyo, Japan. uchikoga@phys.chuo-u.ac.jp
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Uchikoga
authors.forename: Yuri
authors.initials: Y
authors.lastname: Matsuzaki
authors.forename: Masahito
authors.initials: M
authors.lastname: Ohue
authors.forename: Takatsugu
authors.initials: T
authors.lastname: Hirokawa
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Akiyama
mesh_terms: D019295:Computational Biology / Q000379:methods*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins