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SProt: sphere-based protein structure similarity algorithm
BACKGROUND: Similarity search in protein databases is one of the most essential issues in computational proteomics. With the growing number of experimentally resolved protein structures, the focus shifted from sequences to structures. The area of structure similarity forms a big challenge since even...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289081/ https://www.ncbi.nlm.nih.gov/pubmed/22166105 http://dx.doi.org/10.1186/1477-5956-9-S1-S20 |
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author | Galgonek, Jakub Hoksza, David Skopal, Tomáš |
author_facet | Galgonek, Jakub Hoksza, David Skopal, Tomáš |
author_sort | Galgonek, Jakub |
collection | PubMed |
description | BACKGROUND: Similarity search in protein databases is one of the most essential issues in computational proteomics. With the growing number of experimentally resolved protein structures, the focus shifted from sequences to structures. The area of structure similarity forms a big challenge since even no standard definition of optimal structure similarity exists in the field. RESULTS: We propose a protein structure similarity measure called SProt. SProt concentrates on high-quality modeling of local similarity in the process of feature extraction. SProt’s features are based on spherical spatial neighborhood of amino acids where similarity can be well-defined. On top of the partial local similarities, global measure assessing similarity to a pair of protein structures is built. Finally, indexing is applied making the search process by an order of magnitude faster. CONCLUSIONS: The proposed method outperforms other methods in classification accuracy on SCOP superfamily and fold level, while it is at least comparable to the best existing solutions in terms of precision-recall or quality of alignment. |
format | Online Article Text |
id | pubmed-3289081 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-32890812012-02-29 SProt: sphere-based protein structure similarity algorithm Galgonek, Jakub Hoksza, David Skopal, Tomáš Proteome Sci Proceedings BACKGROUND: Similarity search in protein databases is one of the most essential issues in computational proteomics. With the growing number of experimentally resolved protein structures, the focus shifted from sequences to structures. The area of structure similarity forms a big challenge since even no standard definition of optimal structure similarity exists in the field. RESULTS: We propose a protein structure similarity measure called SProt. SProt concentrates on high-quality modeling of local similarity in the process of feature extraction. SProt’s features are based on spherical spatial neighborhood of amino acids where similarity can be well-defined. On top of the partial local similarities, global measure assessing similarity to a pair of protein structures is built. Finally, indexing is applied making the search process by an order of magnitude faster. CONCLUSIONS: The proposed method outperforms other methods in classification accuracy on SCOP superfamily and fold level, while it is at least comparable to the best existing solutions in terms of precision-recall or quality of alignment. BioMed Central 2011-10-14 /pmc/articles/PMC3289081/ /pubmed/22166105 http://dx.doi.org/10.1186/1477-5956-9-S1-S20 Text en Copyright ©2011 Galgonek 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 | Proceedings Galgonek, Jakub Hoksza, David Skopal, Tomáš SProt: sphere-based protein structure similarity algorithm |
title | SProt: sphere-based protein structure similarity algorithm |
title_full | SProt: sphere-based protein structure similarity algorithm |
title_fullStr | SProt: sphere-based protein structure similarity algorithm |
title_full_unstemmed | SProt: sphere-based protein structure similarity algorithm |
title_short | SProt: sphere-based protein structure similarity algorithm |
title_sort | sprot: sphere-based protein structure similarity algorithm |
topic | Proceedings |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289081/ https://www.ncbi.nlm.nih.gov/pubmed/22166105 http://dx.doi.org/10.1186/1477-5956-9-S1-S20 |
work_keys_str_mv | AT galgonekjakub sprotspherebasedproteinstructuresimilarityalgorithm AT hokszadavid sprotspherebasedproteinstructuresimilarityalgorithm AT skopaltomas sprotspherebasedproteinstructuresimilarityalgorithm |