SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information.
In this paper, we describe SAFlex (Structural Alphabet Flexibility), an extension of an existing structural alphabet (HMM-SA), to better explore increasing protein three dimensional structure information by encoding conformations of proteins in case of missing residues or uncertainties. An SA aims t...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC6033379?pdf=render |
| _version_ | 1819261751852531712 |
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| author | Ikram Allam Delphine Flatters Géraldine Caumes Leslie Regad Vincent Delos Gregory Nuel Anne-Claude Camproux |
| author_facet | Ikram Allam Delphine Flatters Géraldine Caumes Leslie Regad Vincent Delos Gregory Nuel Anne-Claude Camproux |
| author_sort | Ikram Allam |
| collection | DOAJ |
| description | In this paper, we describe SAFlex (Structural Alphabet Flexibility), an extension of an existing structural alphabet (HMM-SA), to better explore increasing protein three dimensional structure information by encoding conformations of proteins in case of missing residues or uncertainties. An SA aims to reduce three dimensional conformations of proteins as well as their analysis and comparison complexity by simplifying any conformation in a series of structural letters. Our methodology presents several novelties. Firstly, it can account for the encoding uncertainty by providing a wide range of encoding options: the maximum a posteriori, the marginal posterior distribution, and the effective number of letters at each given position. Secondly, our new algorithm deals with the missing data in the protein structure files (concerning more than 75% of the proteins from the Protein Data Bank) in a rigorous probabilistic framework. Thirdly, SAFlex is able to encode and to build a consensus encoding from different replicates of a single protein such as several homomer chains. This allows localizing structural differences between different chains and detecting structural variability, which is essential for protein flexibility identification. These improvements are illustrated on different proteins, such as the crystal structure of an eukaryotic small heat shock protein. They are promising to explore increasing protein redundancy data and obtain useful quantification of their flexibility. |
| first_indexed | 2024-12-23T19:46:47Z |
| format | Article |
| id | doaj.art-fa4eb1feb90e462489338045fa85ef4d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T19:46:47Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-fa4eb1feb90e462489338045fa85ef4d2022-12-21T17:33:31ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01137e019885410.1371/journal.pone.0198854SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information.Ikram AllamDelphine FlattersGéraldine CaumesLeslie RegadVincent DelosGregory NuelAnne-Claude CamprouxIn this paper, we describe SAFlex (Structural Alphabet Flexibility), an extension of an existing structural alphabet (HMM-SA), to better explore increasing protein three dimensional structure information by encoding conformations of proteins in case of missing residues or uncertainties. An SA aims to reduce three dimensional conformations of proteins as well as their analysis and comparison complexity by simplifying any conformation in a series of structural letters. Our methodology presents several novelties. Firstly, it can account for the encoding uncertainty by providing a wide range of encoding options: the maximum a posteriori, the marginal posterior distribution, and the effective number of letters at each given position. Secondly, our new algorithm deals with the missing data in the protein structure files (concerning more than 75% of the proteins from the Protein Data Bank) in a rigorous probabilistic framework. Thirdly, SAFlex is able to encode and to build a consensus encoding from different replicates of a single protein such as several homomer chains. This allows localizing structural differences between different chains and detecting structural variability, which is essential for protein flexibility identification. These improvements are illustrated on different proteins, such as the crystal structure of an eukaryotic small heat shock protein. They are promising to explore increasing protein redundancy data and obtain useful quantification of their flexibility.http://europepmc.org/articles/PMC6033379?pdf=render |
| spellingShingle | Ikram Allam Delphine Flatters Géraldine Caumes Leslie Regad Vincent Delos Gregory Nuel Anne-Claude Camproux SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. PLoS ONE |
| title | SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. |
| title_full | SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. |
| title_fullStr | SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. |
| title_full_unstemmed | SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. |
| title_short | SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. |
| title_sort | saflex a structural alphabet extension to integrate protein structural flexibility and missing data information |
| url | http://europepmc.org/articles/PMC6033379?pdf=render |
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