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DSP: a protein shape string and its profile prediction server

Many studies have demonstrated that shape string is an extremely important structure representation, since it is more complete than the classical secondary structure. The shape string provides detailed information also in the regions denoted random coil. But few services are provided for systematic...

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Detalles Bibliográficos
Autores principales: Sun, Jiangming, Tang, Shengnan, Xiong, Wenwei, Cong, Peisheng, Li, Tonghua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394270/
https://www.ncbi.nlm.nih.gov/pubmed/22553364
http://dx.doi.org/10.1093/nar/gks361
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author Sun, Jiangming
Tang, Shengnan
Xiong, Wenwei
Cong, Peisheng
Li, Tonghua
author_facet Sun, Jiangming
Tang, Shengnan
Xiong, Wenwei
Cong, Peisheng
Li, Tonghua
author_sort Sun, Jiangming
collection PubMed
description Many studies have demonstrated that shape string is an extremely important structure representation, since it is more complete than the classical secondary structure. The shape string provides detailed information also in the regions denoted random coil. But few services are provided for systematic analysis of protein shape string. To fill this gap, we have developed an accurate shape string predictor based on two innovative technologies: a knowledge-driven sequence alignment and a sequence shape string profile method. The performance on blind test data demonstrates that the proposed method can be used for accurate prediction of protein shape string. The DSP server provides both predicted shape string and sequence shape string profile for each query sequence. Using this information, the users can compare protein structure or display protein evolution in shape string space. The DSP server is available at both http://cheminfo.tongji.edu.cn/dsp/ and its main mirror http://chemcenter.tongji.edu.cn/dsp/.
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spelling pubmed-33942702012-07-30 DSP: a protein shape string and its profile prediction server Sun, Jiangming Tang, Shengnan Xiong, Wenwei Cong, Peisheng Li, Tonghua Nucleic Acids Res Articles Many studies have demonstrated that shape string is an extremely important structure representation, since it is more complete than the classical secondary structure. The shape string provides detailed information also in the regions denoted random coil. But few services are provided for systematic analysis of protein shape string. To fill this gap, we have developed an accurate shape string predictor based on two innovative technologies: a knowledge-driven sequence alignment and a sequence shape string profile method. The performance on blind test data demonstrates that the proposed method can be used for accurate prediction of protein shape string. The DSP server provides both predicted shape string and sequence shape string profile for each query sequence. Using this information, the users can compare protein structure or display protein evolution in shape string space. The DSP server is available at both http://cheminfo.tongji.edu.cn/dsp/ and its main mirror http://chemcenter.tongji.edu.cn/dsp/. Oxford University Press 2012-07 2012-05-02 /pmc/articles/PMC3394270/ /pubmed/22553364 http://dx.doi.org/10.1093/nar/gks361 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Sun, Jiangming
Tang, Shengnan
Xiong, Wenwei
Cong, Peisheng
Li, Tonghua
DSP: a protein shape string and its profile prediction server
title DSP: a protein shape string and its profile prediction server
title_full DSP: a protein shape string and its profile prediction server
title_fullStr DSP: a protein shape string and its profile prediction server
title_full_unstemmed DSP: a protein shape string and its profile prediction server
title_short DSP: a protein shape string and its profile prediction server
title_sort dsp: a protein shape string and its profile prediction server
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394270/
https://www.ncbi.nlm.nih.gov/pubmed/22553364
http://dx.doi.org/10.1093/nar/gks361
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