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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712918/ https://www.ncbi.nlm.nih.gov/pubmed/23874954 http://dx.doi.org/10.1371/journal.pone.0069365 |
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author | Uchikoga, Nobuyuki Matsuzaki, Yuri Ohue, Masahito Hirokawa, Takatsugu Akiyama, Yutaka |
author_facet | Uchikoga, Nobuyuki Matsuzaki, Yuri Ohue, Masahito Hirokawa, Takatsugu Akiyama, Yutaka |
author_sort | Uchikoga, Nobuyuki |
collection | PubMed |
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 | Online Article Text |
id | pubmed-3712918 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-37129182013-07-19 Re-Docking Scheme for Generating Near-Native Protein Complexes by Assembling Residue Interaction Fingerprints Uchikoga, Nobuyuki Matsuzaki, Yuri Ohue, Masahito Hirokawa, Takatsugu Akiyama, Yutaka PLoS One Research Article 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. Public Library of Science 2013-07-16 /pmc/articles/PMC3712918/ /pubmed/23874954 http://dx.doi.org/10.1371/journal.pone.0069365 Text en © 2013 Uchikoga et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Uchikoga, Nobuyuki Matsuzaki, Yuri Ohue, Masahito Hirokawa, Takatsugu Akiyama, Yutaka Re-Docking Scheme for Generating Near-Native Protein Complexes by Assembling Residue Interaction Fingerprints |
title | 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_short | 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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712918/ https://www.ncbi.nlm.nih.gov/pubmed/23874954 http://dx.doi.org/10.1371/journal.pone.0069365 |
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