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Improved protein surface comparison and application to low-resolution protein structure data

BACKGROUND: Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biol...

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Detalles Bibliográficos
Autores principales: Sael, Lee, Kihara, Daisuke
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024873/
https://www.ncbi.nlm.nih.gov/pubmed/21172052
http://dx.doi.org/10.1186/1471-2105-11-S11-S2
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author Sael, Lee
Kihara, Daisuke
author_facet Sael, Lee
Kihara, Daisuke
author_sort Sael, Lee
collection PubMed
description BACKGROUND: Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. RESULTS: The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. CONCLUSIONS: Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy.
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spelling pubmed-30248732011-01-22 Improved protein surface comparison and application to low-resolution protein structure data Sael, Lee Kihara, Daisuke BMC Bioinformatics Research BACKGROUND: Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. RESULTS: The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. CONCLUSIONS: Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy. BioMed Central 2010-12-14 /pmc/articles/PMC3024873/ /pubmed/21172052 http://dx.doi.org/10.1186/1471-2105-11-S11-S2 Text en Copyright ©2010 Kihara and Sael; 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
Sael, Lee
Kihara, Daisuke
Improved protein surface comparison and application to low-resolution protein structure data
title Improved protein surface comparison and application to low-resolution protein structure data
title_full Improved protein surface comparison and application to low-resolution protein structure data
title_fullStr Improved protein surface comparison and application to low-resolution protein structure data
title_full_unstemmed Improved protein surface comparison and application to low-resolution protein structure data
title_short Improved protein surface comparison and application to low-resolution protein structure data
title_sort improved protein surface comparison and application to low-resolution protein structure data
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024873/
https://www.ncbi.nlm.nih.gov/pubmed/21172052
http://dx.doi.org/10.1186/1471-2105-11-S11-S2
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