Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database

We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kap...

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Detalles Bibliográficos
Autores principales: Tung, Chi-Hua, Huang, Jhang-Wei, Yang, Jinn-Moon
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868941/
https://www.ncbi.nlm.nih.gov/pubmed/17335583
http://dx.doi.org/10.1186/gb-2007-8-3-r31
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author Tung, Chi-Hua
Huang, Jhang-Wei
Yang, Jinn-Moon
author_facet Tung, Chi-Hua
Huang, Jhang-Wei
Yang, Jinn-Moon
author_sort Tung, Chi-Hua
collection PubMed
description We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (κ, α) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity.
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spelling pubmed-18689412007-05-16 Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database Tung, Chi-Hua Huang, Jhang-Wei Yang, Jinn-Moon Genome Biol Method We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (κ, α) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity. BioMed Central 2007 2007-03-03 /pmc/articles/PMC1868941/ /pubmed/17335583 http://dx.doi.org/10.1186/gb-2007-8-3-r31 Text en Copyright ©2007 Tung 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 Method
Tung, Chi-Hua
Huang, Jhang-Wei
Yang, Jinn-Moon
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
title Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
title_full Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
title_fullStr Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
title_full_unstemmed Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
title_short Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
title_sort kappa-alpha plot derived structural alphabet and blosum-like substitution matrix for rapid search of protein structure database
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868941/
https://www.ncbi.nlm.nih.gov/pubmed/17335583
http://dx.doi.org/10.1186/gb-2007-8-3-r31
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AT yangjinnmoon kappaalphaplotderivedstructuralalphabetandblosumlikesubstitutionmatrixforrapidsearchofproteinstructuredatabase

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