Protein alignment based on higher order conditional random fields for template-based modeling.
The query-template alignment of proteins is one of the most critical steps of template-based modeling methods used to predict the 3D structure of a query protein. This alignment can be interpreted as a temporal classification or structured prediction task and first order Conditional Random Fields ha...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5983487?pdf=render |
| _version_ | 1819151938560720896 |
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| author | Juan A Morales-Cordovilla Victoria Sanchez Martin Ratajczak |
| author_facet | Juan A Morales-Cordovilla Victoria Sanchez Martin Ratajczak |
| author_sort | Juan A Morales-Cordovilla |
| collection | DOAJ |
| description | The query-template alignment of proteins is one of the most critical steps of template-based modeling methods used to predict the 3D structure of a query protein. This alignment can be interpreted as a temporal classification or structured prediction task and first order Conditional Random Fields have been proposed for protein alignment and proven to be rather successful. Some other popular structured prediction problems, such as speech or image classification, have gained from the use of higher order Conditional Random Fields due to the well known higher order correlations that exist between their labels and features. In this paper, we propose and describe the use of higher order Conditional Random Fields for query-template protein alignment. The experiments carried out on different public datasets validate our proposal, especially on distantly-related protein pairs which are the most difficult to align. |
| first_indexed | 2024-12-22T14:41:21Z |
| format | Article |
| id | doaj.art-f4dd2c8d8a224b3b84c088cb6375c5bb |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T14:41:21Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f4dd2c8d8a224b3b84c088cb6375c5bb2022-12-21T18:22:32ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01136e019791210.1371/journal.pone.0197912Protein alignment based on higher order conditional random fields for template-based modeling.Juan A Morales-CordovillaVictoria SanchezMartin RatajczakThe query-template alignment of proteins is one of the most critical steps of template-based modeling methods used to predict the 3D structure of a query protein. This alignment can be interpreted as a temporal classification or structured prediction task and first order Conditional Random Fields have been proposed for protein alignment and proven to be rather successful. Some other popular structured prediction problems, such as speech or image classification, have gained from the use of higher order Conditional Random Fields due to the well known higher order correlations that exist between their labels and features. In this paper, we propose and describe the use of higher order Conditional Random Fields for query-template protein alignment. The experiments carried out on different public datasets validate our proposal, especially on distantly-related protein pairs which are the most difficult to align.http://europepmc.org/articles/PMC5983487?pdf=render |
| spellingShingle | Juan A Morales-Cordovilla Victoria Sanchez Martin Ratajczak Protein alignment based on higher order conditional random fields for template-based modeling. PLoS ONE |
| title | Protein alignment based on higher order conditional random fields for template-based modeling. |
| title_full | Protein alignment based on higher order conditional random fields for template-based modeling. |
| title_fullStr | Protein alignment based on higher order conditional random fields for template-based modeling. |
| title_full_unstemmed | Protein alignment based on higher order conditional random fields for template-based modeling. |
| title_short | Protein alignment based on higher order conditional random fields for template-based modeling. |
| title_sort | protein alignment based on higher order conditional random fields for template based modeling |
| url | http://europepmc.org/articles/PMC5983487?pdf=render |
| work_keys_str_mv | AT juanamoralescordovilla proteinalignmentbasedonhigherorderconditionalrandomfieldsfortemplatebasedmodeling AT victoriasanchez proteinalignmentbasedonhigherorderconditionalrandomfieldsfortemplatebasedmodeling AT martinratajczak proteinalignmentbasedonhigherorderconditionalrandomfieldsfortemplatebasedmodeling |