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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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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/. |
format | Online Article Text |
id | pubmed-3394270 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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