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Rapid detection of similarity in protein structure and function through contact metric distances

The characterization of biological function among newly determined protein structures is a central challenge in structural genomics. One class of computational solutions to this problem is based on the similarity of protein structure. Here, we implement a simple yet efficient measure of protein stru...

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Detalles Bibliográficos
Autores principales: Lisewski, Andreas Martin, Lichtarge, Olivier
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1702494/
https://www.ncbi.nlm.nih.gov/pubmed/17130161
http://dx.doi.org/10.1093/nar/gkl788
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author Lisewski, Andreas Martin
Lichtarge, Olivier
author_facet Lisewski, Andreas Martin
Lichtarge, Olivier
author_sort Lisewski, Andreas Martin
collection PubMed
description The characterization of biological function among newly determined protein structures is a central challenge in structural genomics. One class of computational solutions to this problem is based on the similarity of protein structure. Here, we implement a simple yet efficient measure of protein structure similarity, the contact metric. Even though its computation avoids structural alignments and is therefore nearly instantaneous, we find that small values correlate with geometrical root mean square deviations obtained from structural alignments. To test whether the contact metric detects functional similarity, as defined by Gene Ontology (GO) terms, it was compared in large-scale computational experiments to four other measures of structural similarity, including alignment algorithms as well as alignment independent approaches. The contact metric was the fastest method and its sensitivity, at any given specificity level, was a close second only to Fast Alignment and Search Tool—a structural alignment method that is slower by three orders of magnitude. Critically, nearly 40% of correct functional inferences by the contact metric were not identified by any other approach, which shows that the contact metric is complementary and computationally efficient in detecting functional relationships between proteins. A public ‘Contact Metric Internet Server’ is provided.
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spelling pubmed-17024942006-12-26 Rapid detection of similarity in protein structure and function through contact metric distances Lisewski, Andreas Martin Lichtarge, Olivier Nucleic Acids Res Methods Online The characterization of biological function among newly determined protein structures is a central challenge in structural genomics. One class of computational solutions to this problem is based on the similarity of protein structure. Here, we implement a simple yet efficient measure of protein structure similarity, the contact metric. Even though its computation avoids structural alignments and is therefore nearly instantaneous, we find that small values correlate with geometrical root mean square deviations obtained from structural alignments. To test whether the contact metric detects functional similarity, as defined by Gene Ontology (GO) terms, it was compared in large-scale computational experiments to four other measures of structural similarity, including alignment algorithms as well as alignment independent approaches. The contact metric was the fastest method and its sensitivity, at any given specificity level, was a close second only to Fast Alignment and Search Tool—a structural alignment method that is slower by three orders of magnitude. Critically, nearly 40% of correct functional inferences by the contact metric were not identified by any other approach, which shows that the contact metric is complementary and computationally efficient in detecting functional relationships between proteins. A public ‘Contact Metric Internet Server’ is provided. Oxford University Press 2006-12 2006-11-27 /pmc/articles/PMC1702494/ /pubmed/17130161 http://dx.doi.org/10.1093/nar/gkl788 Text en © 2006 The Author(s).
spellingShingle Methods Online
Lisewski, Andreas Martin
Lichtarge, Olivier
Rapid detection of similarity in protein structure and function through contact metric distances
title Rapid detection of similarity in protein structure and function through contact metric distances
title_full Rapid detection of similarity in protein structure and function through contact metric distances
title_fullStr Rapid detection of similarity in protein structure and function through contact metric distances
title_full_unstemmed Rapid detection of similarity in protein structure and function through contact metric distances
title_short Rapid detection of similarity in protein structure and function through contact metric distances
title_sort rapid detection of similarity in protein structure and function through contact metric distances
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1702494/
https://www.ncbi.nlm.nih.gov/pubmed/17130161
http://dx.doi.org/10.1093/nar/gkl788
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