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Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features
BACKGROUND: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining hi...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120151/ https://www.ncbi.nlm.nih.gov/pubmed/25080939 http://dx.doi.org/10.1186/1471-2105-15-S8-S3 |
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author | Yaseen, Ashraf Li, Yaohang |
author_facet | Yaseen, Ashraf Li, Yaohang |
author_sort | Yaseen, Ashraf |
collection | PubMed |
description | BACKGROUND: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models. METHODS: In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. RESULTS: After applying the template-based 8-state secondary structure prediction method, the 7-fold cross-validated Q8 accuracy is 78.85%. Even templates from structures with only 20%~30% sequence similarity can help improve the 8-state prediction accuracy. More importantly, when good templates are available, the prediction accuracy of less frequent secondary structures, such as 3-10 helices, turns, and bends, are highly improved, which are useful for practical applications. CONCLUSIONS: Our computational results show that the templates containing structural information are effective features to enhance 8-state secondary structure predictions. Our prediction algorithm is implemented on a web server named "C8-SCORPION" available at: http://hpcr.cs.odu.edu/c8scorpion. |
format | Online Article Text |
id | pubmed-4120151 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41201512014-08-11 Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features Yaseen, Ashraf Li, Yaohang BMC Bioinformatics Research BACKGROUND: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models. METHODS: In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. RESULTS: After applying the template-based 8-state secondary structure prediction method, the 7-fold cross-validated Q8 accuracy is 78.85%. Even templates from structures with only 20%~30% sequence similarity can help improve the 8-state prediction accuracy. More importantly, when good templates are available, the prediction accuracy of less frequent secondary structures, such as 3-10 helices, turns, and bends, are highly improved, which are useful for practical applications. CONCLUSIONS: Our computational results show that the templates containing structural information are effective features to enhance 8-state secondary structure predictions. Our prediction algorithm is implemented on a web server named "C8-SCORPION" available at: http://hpcr.cs.odu.edu/c8scorpion. BioMed Central 2014-07-14 /pmc/articles/PMC4120151/ /pubmed/25080939 http://dx.doi.org/10.1186/1471-2105-15-S8-S3 Text en Copyright © 2014 Yaseen and Li; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Yaseen, Ashraf Li, Yaohang Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features |
title | Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features |
title_full | Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features |
title_fullStr | Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features |
title_full_unstemmed | Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features |
title_short | Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features |
title_sort | template-based c8-scorpion: a protein 8-state secondary structure prediction method using structural information and context-based features |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120151/ https://www.ncbi.nlm.nih.gov/pubmed/25080939 http://dx.doi.org/10.1186/1471-2105-15-S8-S3 |
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