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Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments

Proteins often exist as their multimeric forms when they function as so‐called biological assemblies consisting of the specific number and arrangement of protein subunits. Consequently, elucidating biological assemblies is necessary to improve understanding of protein function. Template‐Based Modeli...

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Autores principales: Nakamura, Tsukasa, Oda, Toshiyuki, Fukasawa, Yoshinori, Tomii, Kentaro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836938/
https://www.ncbi.nlm.nih.gov/pubmed/29178285
http://dx.doi.org/10.1002/prot.25432
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author Nakamura, Tsukasa
Oda, Toshiyuki
Fukasawa, Yoshinori
Tomii, Kentaro
author_facet Nakamura, Tsukasa
Oda, Toshiyuki
Fukasawa, Yoshinori
Tomii, Kentaro
author_sort Nakamura, Tsukasa
collection PubMed
description Proteins often exist as their multimeric forms when they function as so‐called biological assemblies consisting of the specific number and arrangement of protein subunits. Consequently, elucidating biological assemblies is necessary to improve understanding of protein function. Template‐Based Modeling (TBM), based on known protein structures, has been used widely for protein structure prediction. Actually, TBM has become an increasingly useful approach in recent years because of the increased amounts of information related to protein amino acid sequences and three‐dimensional structures. An apparently similar situation exists for biological assembly structure prediction as protein complex structures in the PDB increase, although the inference of biological assemblies is not a trivial task. Many methods using TBM, including ours, have been developed for protein structure prediction. Using enhanced profile–profile alignments, we participated in the 12th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP12), as the FONT team (Group # 480). Herein, we present experimental procedures and results of retrospective analyses using our approach for the Quaternary Structure Prediction category of CASP12. We performed profile–profile alignments of several types, based on FORTE, our profile–profile alignment algorithm, to identify suitable templates. Results show that these alignment results enable us to find templates in almost all possible cases. Moreover, we have come to understand the necessity of developing a model selection method that provides improved accuracy. Results also demonstrate that, to some extent, finding templates of protein complexes is useful even for MEDIUM and HARD assembly prediction.
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spelling pubmed-58369382018-03-12 Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments Nakamura, Tsukasa Oda, Toshiyuki Fukasawa, Yoshinori Tomii, Kentaro Proteins Research Articles Proteins often exist as their multimeric forms when they function as so‐called biological assemblies consisting of the specific number and arrangement of protein subunits. Consequently, elucidating biological assemblies is necessary to improve understanding of protein function. Template‐Based Modeling (TBM), based on known protein structures, has been used widely for protein structure prediction. Actually, TBM has become an increasingly useful approach in recent years because of the increased amounts of information related to protein amino acid sequences and three‐dimensional structures. An apparently similar situation exists for biological assembly structure prediction as protein complex structures in the PDB increase, although the inference of biological assemblies is not a trivial task. Many methods using TBM, including ours, have been developed for protein structure prediction. Using enhanced profile–profile alignments, we participated in the 12th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP12), as the FONT team (Group # 480). Herein, we present experimental procedures and results of retrospective analyses using our approach for the Quaternary Structure Prediction category of CASP12. We performed profile–profile alignments of several types, based on FORTE, our profile–profile alignment algorithm, to identify suitable templates. Results show that these alignment results enable us to find templates in almost all possible cases. Moreover, we have come to understand the necessity of developing a model selection method that provides improved accuracy. Results also demonstrate that, to some extent, finding templates of protein complexes is useful even for MEDIUM and HARD assembly prediction. John Wiley and Sons Inc. 2017-12-05 2018-03 /pmc/articles/PMC5836938/ /pubmed/29178285 http://dx.doi.org/10.1002/prot.25432 Text en © 2017 The Authors Proteins: Structure, Function and Bioinformatics Published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial (http://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Research Articles
Nakamura, Tsukasa
Oda, Toshiyuki
Fukasawa, Yoshinori
Tomii, Kentaro
Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments
title Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments
title_full Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments
title_fullStr Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments
title_full_unstemmed Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments
title_short Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments
title_sort template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836938/
https://www.ncbi.nlm.nih.gov/pubmed/29178285
http://dx.doi.org/10.1002/prot.25432
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