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Prediction of enzyme function by combining sequence similarity and protein interactions

BACKGROUND: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar...

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Autores principales: Espadaler, Jordi, Eswar, Narayanan, Querol, Enrique, Avilés, Francesc X, Sali, Andrej, Marti-Renom, Marc A, Oliva, Baldomero
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430716/
https://www.ncbi.nlm.nih.gov/pubmed/18505562
http://dx.doi.org/10.1186/1471-2105-9-249
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author Espadaler, Jordi
Eswar, Narayanan
Querol, Enrique
Avilés, Francesc X
Sali, Andrej
Marti-Renom, Marc A
Oliva, Baldomero
author_facet Espadaler, Jordi
Eswar, Narayanan
Querol, Enrique
Avilés, Francesc X
Sali, Andrej
Marti-Renom, Marc A
Oliva, Baldomero
author_sort Espadaler, Jordi
collection PubMed
description BACKGROUND: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners. RESULTS: The method has been tested against the PSI-BLAST program using a set of 3,890 protein sequences from which interaction data was available. For protein sequences that align with at least 40% sequence identity to a known enzyme, the specificity of our method in predicting the first three EC digits increased from 80% to 90% at 80% coverage when compared to PSI-BLAST. CONCLUSION: Our method can also be used in proteins for which homologous sequences with known interacting partners can be detected. Thus, our method could increase 10% the specificity of genome-wide enzyme predictions based on sequence matching by PSI-BLAST alone.
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spelling pubmed-24307162008-06-19 Prediction of enzyme function by combining sequence similarity and protein interactions Espadaler, Jordi Eswar, Narayanan Querol, Enrique Avilés, Francesc X Sali, Andrej Marti-Renom, Marc A Oliva, Baldomero BMC Bioinformatics Methodology Article BACKGROUND: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners. RESULTS: The method has been tested against the PSI-BLAST program using a set of 3,890 protein sequences from which interaction data was available. For protein sequences that align with at least 40% sequence identity to a known enzyme, the specificity of our method in predicting the first three EC digits increased from 80% to 90% at 80% coverage when compared to PSI-BLAST. CONCLUSION: Our method can also be used in proteins for which homologous sequences with known interacting partners can be detected. Thus, our method could increase 10% the specificity of genome-wide enzyme predictions based on sequence matching by PSI-BLAST alone. BioMed Central 2008-05-27 /pmc/articles/PMC2430716/ /pubmed/18505562 http://dx.doi.org/10.1186/1471-2105-9-249 Text en Copyright © 2008 Espadaler et al; 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 Methodology Article
Espadaler, Jordi
Eswar, Narayanan
Querol, Enrique
Avilés, Francesc X
Sali, Andrej
Marti-Renom, Marc A
Oliva, Baldomero
Prediction of enzyme function by combining sequence similarity and protein interactions
title Prediction of enzyme function by combining sequence similarity and protein interactions
title_full Prediction of enzyme function by combining sequence similarity and protein interactions
title_fullStr Prediction of enzyme function by combining sequence similarity and protein interactions
title_full_unstemmed Prediction of enzyme function by combining sequence similarity and protein interactions
title_short Prediction of enzyme function by combining sequence similarity and protein interactions
title_sort prediction of enzyme function by combining sequence similarity and protein interactions
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430716/
https://www.ncbi.nlm.nih.gov/pubmed/18505562
http://dx.doi.org/10.1186/1471-2105-9-249
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