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An Algorithm for Protein Helix Assignment Using Helix Geometry

Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment pr...

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Detalles Bibliográficos
Autores principales: Cao, Chen, Xu, Shutan, Wang, Lincong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488512/
https://www.ncbi.nlm.nih.gov/pubmed/26132394
http://dx.doi.org/10.1371/journal.pone.0129674
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author Cao, Chen
Xu, Shutan
Wang, Lincong
author_facet Cao, Chen
Xu, Shutan
Wang, Lincong
author_sort Cao, Chen
collection PubMed
description Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone C(α) atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 3(10) and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins.
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spelling pubmed-44885122015-07-14 An Algorithm for Protein Helix Assignment Using Helix Geometry Cao, Chen Xu, Shutan Wang, Lincong PLoS One Research Article Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone C(α) atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 3(10) and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins. Public Library of Science 2015-07-01 /pmc/articles/PMC4488512/ /pubmed/26132394 http://dx.doi.org/10.1371/journal.pone.0129674 Text en © 2015 Cao et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Cao, Chen
Xu, Shutan
Wang, Lincong
An Algorithm for Protein Helix Assignment Using Helix Geometry
title An Algorithm for Protein Helix Assignment Using Helix Geometry
title_full An Algorithm for Protein Helix Assignment Using Helix Geometry
title_fullStr An Algorithm for Protein Helix Assignment Using Helix Geometry
title_full_unstemmed An Algorithm for Protein Helix Assignment Using Helix Geometry
title_short An Algorithm for Protein Helix Assignment Using Helix Geometry
title_sort algorithm for protein helix assignment using helix geometry
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488512/
https://www.ncbi.nlm.nih.gov/pubmed/26132394
http://dx.doi.org/10.1371/journal.pone.0129674
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