Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification

BACKGROUND: Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to di...

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Autores principales: Zotenko, Elena, O'Leary, Dianne P, Przytycka, Teresa M
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526735/
https://www.ncbi.nlm.nih.gov/pubmed/16762072
http://dx.doi.org/10.1186/1472-6807-6-12
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author Zotenko, Elena
O'Leary, Dianne P
Przytycka, Teresa M
author_facet Zotenko, Elena
O'Leary, Dianne P
Przytycka, Teresa M
author_sort Zotenko, Elena
collection PubMed
description BACKGROUND: Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to distance computation between corresponding vectors. As structural similarity is approximated by distance between projections, the success of any projection method depends on how well its mapping function is able to capture the salient features of protein structure. There is no agreement on what constitutes a good projection technique and the three currently known projection methods utilize very different approaches to the mapping construction, both in terms of what structural elements are included and how this information is integrated to produce a vector representation. RESULTS: In this paper we propose a novel projection method that uses secondary structure information to produce the mapping. First, a diverse set of spatial arrangements of triplets of secondary structure elements, a set of structural models, is automatically selected. Then, each protein structure is mapped into a high-dimensional vector of "counts" or footprint, where each count corresponds to the number of times a given structural model is observed in the structure, weighted by the precision with which the model is reproduced. We perform the first comprehensive evaluation of our method together with all other currently known projection methods. CONCLUSION: The results of our evaluation suggest that the type of structural information used by a projection method affects the ability of the method to detect structural similarity. In particular, our method that uses the spatial conformations of triplets of secondary structure elements outperforms other methods in most of the tests.
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spelling pubmed-15267352006-08-07 Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification Zotenko, Elena O'Leary, Dianne P Przytycka, Teresa M BMC Struct Biol Research Article BACKGROUND: Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to distance computation between corresponding vectors. As structural similarity is approximated by distance between projections, the success of any projection method depends on how well its mapping function is able to capture the salient features of protein structure. There is no agreement on what constitutes a good projection technique and the three currently known projection methods utilize very different approaches to the mapping construction, both in terms of what structural elements are included and how this information is integrated to produce a vector representation. RESULTS: In this paper we propose a novel projection method that uses secondary structure information to produce the mapping. First, a diverse set of spatial arrangements of triplets of secondary structure elements, a set of structural models, is automatically selected. Then, each protein structure is mapped into a high-dimensional vector of "counts" or footprint, where each count corresponds to the number of times a given structural model is observed in the structure, weighted by the precision with which the model is reproduced. We perform the first comprehensive evaluation of our method together with all other currently known projection methods. CONCLUSION: The results of our evaluation suggest that the type of structural information used by a projection method affects the ability of the method to detect structural similarity. In particular, our method that uses the spatial conformations of triplets of secondary structure elements outperforms other methods in most of the tests. BioMed Central 2006-06-08 /pmc/articles/PMC1526735/ /pubmed/16762072 http://dx.doi.org/10.1186/1472-6807-6-12 Text en Copyright © 2006 Zotenko 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 Research Article
Zotenko, Elena
O'Leary, Dianne P
Przytycka, Teresa M
Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
title Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
title_full Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
title_fullStr Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
title_full_unstemmed Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
title_short Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
title_sort secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526735/
https://www.ncbi.nlm.nih.gov/pubmed/16762072
http://dx.doi.org/10.1186/1472-6807-6-12
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