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Exploring protein structural dissimilarity to facilitate structure classification

BACKGROUND: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classification of Proteins (SCOP), automation has receiv...

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Autores principales: Jain, Pooja, Hirst, Jonathan D
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754988/
https://www.ncbi.nlm.nih.gov/pubmed/19765314
http://dx.doi.org/10.1186/1472-6807-9-60
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author Jain, Pooja
Hirst, Jonathan D
author_facet Jain, Pooja
Hirst, Jonathan D
author_sort Jain, Pooja
collection PubMed
description BACKGROUND: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classification of Proteins (SCOP), automation has received particular attention. Herein, we predict the deepest SCOP structural level that an unclassified protein shares with classified proteins with an equal number of secondary structure elements (SSEs). RESULTS: We compute a coefficient of dissimilarity (Ω) between proteins, based on structural and sequence-based descriptors characterising the respective constituent SSEs. For a set of 1,661 pairs of proteins with sequence identity up to 35%, the performance of Ω in predicting shared Class, Fold and Super-family levels is comparable to that of DaliLite Z score and shows a greater than four-fold increase in the true positive rate (TPR) for proteins sharing the Family level. On a larger set of 600 domains representing 200 families, the performance of Z score improves in predicting a shared Family, but still only achieves about half of the TPR of Ω. The TPR for structures sharing a Super-family is lower than in the first dataset, but Ω performs slightly better than Z score. Overall, the sensitivity of Ω in predicting common Fold level is higher than that of the DaliLite Z score. CONCLUSION: Classification to a deeper level in the hierarchy is specific and difficult. So the efficiency of Ω may be attractive to the curators and the end-users of SCOP. We suggest Ω may be a better measure for structure classification than the DaliLite Z score, with the caveat that currently we are restricted to comparing structures with equal number of SSEs.
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spelling pubmed-27549882009-10-01 Exploring protein structural dissimilarity to facilitate structure classification Jain, Pooja Hirst, Jonathan D BMC Struct Biol Research Article BACKGROUND: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classification of Proteins (SCOP), automation has received particular attention. Herein, we predict the deepest SCOP structural level that an unclassified protein shares with classified proteins with an equal number of secondary structure elements (SSEs). RESULTS: We compute a coefficient of dissimilarity (Ω) between proteins, based on structural and sequence-based descriptors characterising the respective constituent SSEs. For a set of 1,661 pairs of proteins with sequence identity up to 35%, the performance of Ω in predicting shared Class, Fold and Super-family levels is comparable to that of DaliLite Z score and shows a greater than four-fold increase in the true positive rate (TPR) for proteins sharing the Family level. On a larger set of 600 domains representing 200 families, the performance of Z score improves in predicting a shared Family, but still only achieves about half of the TPR of Ω. The TPR for structures sharing a Super-family is lower than in the first dataset, but Ω performs slightly better than Z score. Overall, the sensitivity of Ω in predicting common Fold level is higher than that of the DaliLite Z score. CONCLUSION: Classification to a deeper level in the hierarchy is specific and difficult. So the efficiency of Ω may be attractive to the curators and the end-users of SCOP. We suggest Ω may be a better measure for structure classification than the DaliLite Z score, with the caveat that currently we are restricted to comparing structures with equal number of SSEs. BioMed Central 2009-09-19 /pmc/articles/PMC2754988/ /pubmed/19765314 http://dx.doi.org/10.1186/1472-6807-9-60 Text en Copyright © 2009 Jain and Hirst; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Jain, Pooja
Hirst, Jonathan D
Exploring protein structural dissimilarity to facilitate structure classification
title Exploring protein structural dissimilarity to facilitate structure classification
title_full Exploring protein structural dissimilarity to facilitate structure classification
title_fullStr Exploring protein structural dissimilarity to facilitate structure classification
title_full_unstemmed Exploring protein structural dissimilarity to facilitate structure classification
title_short Exploring protein structural dissimilarity to facilitate structure classification
title_sort exploring protein structural dissimilarity to facilitate structure classification
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754988/
https://www.ncbi.nlm.nih.gov/pubmed/19765314
http://dx.doi.org/10.1186/1472-6807-9-60
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