Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

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 wh...

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Autores principales:	Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/adff15c05a574234a4a550461cedf42a
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spelling	oai:doaj.org-article:adff15c05a574234a4a550461cedf42a2021-11-18T07:37:28ZRe-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.1932-620310.1371/journal.pone.0069365https://doaj.org/article/adff15c05a574234a4a550461cedf42a2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23874954/?tool=EBIhttps://doaj.org/toc/1932-6203Interaction 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.Nobuyuki UchikogaYuri MatsuzakiMasahito OhueTakatsugu HirokawaYutaka AkiyamaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e69365 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nobuyuki Uchikoga Yuri Matsuzaki Masahito Ohue Takatsugu Hirokawa Yutaka Akiyama Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
description	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.
format	article
author	Nobuyuki Uchikoga Yuri Matsuzaki Masahito Ohue Takatsugu Hirokawa Yutaka Akiyama
author_facet	Nobuyuki Uchikoga Yuri Matsuzaki Masahito Ohue Takatsugu Hirokawa Yutaka Akiyama
author_sort	Nobuyuki Uchikoga
title	Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
title_short	Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
title_full	Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
title_fullStr	Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
title_full_unstemmed	Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
title_sort	re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/adff15c05a574234a4a550461cedf42a
work_keys_str_mv	AT nobuyukiuchikoga redockingschemeforgeneratingnearnativeproteincomplexesbyassemblingresidueinteractionfingerprints AT yurimatsuzaki redockingschemeforgeneratingnearnativeproteincomplexesbyassemblingresidueinteractionfingerprints AT masahitoohue redockingschemeforgeneratingnearnativeproteincomplexesbyassemblingresidueinteractionfingerprints AT takatsuguhirokawa redockingschemeforgeneratingnearnativeproteincomplexesbyassemblingresidueinteractionfingerprints AT yutakaakiyama redockingschemeforgeneratingnearnativeproteincomplexesbyassemblingresidueinteractionfingerprints
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Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

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