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Contingency Table Browser − prediction of early stage protein structure
The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-s...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Biomedical Informatics
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658648/ https://www.ncbi.nlm.nih.gov/pubmed/26664034 http://dx.doi.org/10.6026/97320630011486 |
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author | Kalinowska, Barbara Krzykalski, Artur Roterman, Irena |
author_facet | Kalinowska, Barbara Krzykalski, Artur Roterman, Irena |
author_sort | Kalinowska, Barbara |
collection | PubMed |
description | The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-structure relationship information contained in the so-called contingency table − this table expresses the likelihood of encountering various structural motifs for each tetrapeptide fragment in the amino acid sequence. The limited accuracy with which such structures could previously be predicted provided the motivation for a more indepth study of the contingency table itself. The Contingency Table Browser is a tool which can visualize, search and analyze the table. Our work presents possible applications of Contingency Table Browser, among them − analysis of specific protein sequences from the point of view of their structural ambiguity. |
format | Online Article Text |
id | pubmed-4658648 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Biomedical Informatics |
record_format | MEDLINE/PubMed |
spelling | pubmed-46586482015-12-09 Contingency Table Browser − prediction of early stage protein structure Kalinowska, Barbara Krzykalski, Artur Roterman, Irena Bioinformation Server The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-structure relationship information contained in the so-called contingency table − this table expresses the likelihood of encountering various structural motifs for each tetrapeptide fragment in the amino acid sequence. The limited accuracy with which such structures could previously be predicted provided the motivation for a more indepth study of the contingency table itself. The Contingency Table Browser is a tool which can visualize, search and analyze the table. Our work presents possible applications of Contingency Table Browser, among them − analysis of specific protein sequences from the point of view of their structural ambiguity. Biomedical Informatics 2015-10-31 /pmc/articles/PMC4658648/ /pubmed/26664034 http://dx.doi.org/10.6026/97320630011486 Text en © 2015 Biomedical Informatics This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |
spellingShingle | Server Kalinowska, Barbara Krzykalski, Artur Roterman, Irena Contingency Table Browser − prediction of early stage protein structure |
title | Contingency Table Browser − prediction of early stage protein structure |
title_full | Contingency Table Browser − prediction of early stage protein structure |
title_fullStr | Contingency Table Browser − prediction of early stage protein structure |
title_full_unstemmed | Contingency Table Browser − prediction of early stage protein structure |
title_short | Contingency Table Browser − prediction of early stage protein structure |
title_sort | contingency table browser − prediction of early stage protein structure |
topic | Server |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658648/ https://www.ncbi.nlm.nih.gov/pubmed/26664034 http://dx.doi.org/10.6026/97320630011486 |
work_keys_str_mv | AT kalinowskabarbara contingencytablebrowserpredictionofearlystageproteinstructure AT krzykalskiartur contingencytablebrowserpredictionofearlystageproteinstructure AT rotermanirena contingencytablebrowserpredictionofearlystageproteinstructure |