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fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies

The fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. This server uses 3D-BLAST to scan quickly a large structural classification database (SCOP1.71 with <95% identity with each other) and the top 10...

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Detalles Bibliográficos
Autores principales: Tung, Chi-Hua, Yang, Jinn-Moon
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933144/
https://www.ncbi.nlm.nih.gov/pubmed/17485476
http://dx.doi.org/10.1093/nar/gkm288
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author Tung, Chi-Hua
Yang, Jinn-Moon
author_facet Tung, Chi-Hua
Yang, Jinn-Moon
author_sort Tung, Chi-Hua
collection PubMed
description The fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. This server uses 3D-BLAST to scan quickly a large structural classification database (SCOP1.71 with <95% identity with each other) and the top 10 hit domains, which have different superfamily classifications, are obtained from the hit lists. MAMMOTH, a detailed structural alignment tool, is adopted to align these top 10 structures to refine domain boundaries and to identify evolutionary superfamilies. Our previous works demonstrated that 3D-BLAST is as fast as BLAST, and has the characteristics of BLAST (e.g. a robust statistical basis, effective search and reliable database search capabilities) in large structural database searches based on a structural alphabet database and a structural alphabet substitution matrix. The classification accuracy of this server is ∼98% for 586 query structures and the average execution time is ∼5. This server was also evaluated on 8700 structures, which have no annotations in the SCOP; the server can automatically assign 7311 (84%) proteins (9420 domains) to the SCOP superfamilies in 9.6 h. These results suggest that the fastSCOP is robust and can be a useful server for recognizing the evolutionary classifications and the protein functions of novel structures. The server is accessible at http://fastSCOP.life.nctu.edu.tw.
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spelling pubmed-19331442007-07-31 fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies Tung, Chi-Hua Yang, Jinn-Moon Nucleic Acids Res Articles The fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. This server uses 3D-BLAST to scan quickly a large structural classification database (SCOP1.71 with <95% identity with each other) and the top 10 hit domains, which have different superfamily classifications, are obtained from the hit lists. MAMMOTH, a detailed structural alignment tool, is adopted to align these top 10 structures to refine domain boundaries and to identify evolutionary superfamilies. Our previous works demonstrated that 3D-BLAST is as fast as BLAST, and has the characteristics of BLAST (e.g. a robust statistical basis, effective search and reliable database search capabilities) in large structural database searches based on a structural alphabet database and a structural alphabet substitution matrix. The classification accuracy of this server is ∼98% for 586 query structures and the average execution time is ∼5. This server was also evaluated on 8700 structures, which have no annotations in the SCOP; the server can automatically assign 7311 (84%) proteins (9420 domains) to the SCOP superfamilies in 9.6 h. These results suggest that the fastSCOP is robust and can be a useful server for recognizing the evolutionary classifications and the protein functions of novel structures. The server is accessible at http://fastSCOP.life.nctu.edu.tw. Oxford University Press 2007-07 2007-05-07 /pmc/articles/PMC1933144/ /pubmed/17485476 http://dx.doi.org/10.1093/nar/gkm288 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Tung, Chi-Hua
Yang, Jinn-Moon
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies
title fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies
title_full fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies
title_fullStr fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies
title_full_unstemmed fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies
title_short fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies
title_sort fastscop: a fast web server for recognizing protein structural domains and scop superfamilies
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933144/
https://www.ncbi.nlm.nih.gov/pubmed/17485476
http://dx.doi.org/10.1093/nar/gkm288
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