Cargando…
A New Secondary Structure Assignment Algorithm Using C(α) Backbone Fragments
The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on C(α) fragments), for secondary structure element (SSE) assignment based on the alignment of C(α) b...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813195/ https://www.ncbi.nlm.nih.gov/pubmed/26978354 http://dx.doi.org/10.3390/ijms17030333 |
_version_ | 1782424260849958912 |
---|---|
author | Cao, Chen Wang, Guishen Liu, An Xu, Shutan Wang, Lincong Zou, Shuxue |
author_facet | Cao, Chen Wang, Guishen Liu, An Xu, Shutan Wang, Lincong Zou, Shuxue |
author_sort | Cao, Chen |
collection | PubMed |
description | The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on C(α) fragments), for secondary structure element (SSE) assignment based on the alignment of C(α) backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (3(10)-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. |
format | Online Article Text |
id | pubmed-4813195 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-48131952016-04-06 A New Secondary Structure Assignment Algorithm Using C(α) Backbone Fragments Cao, Chen Wang, Guishen Liu, An Xu, Shutan Wang, Lincong Zou, Shuxue Int J Mol Sci Article The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on C(α) fragments), for secondary structure element (SSE) assignment based on the alignment of C(α) backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (3(10)-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. MDPI 2016-03-11 /pmc/articles/PMC4813195/ /pubmed/26978354 http://dx.doi.org/10.3390/ijms17030333 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Cao, Chen Wang, Guishen Liu, An Xu, Shutan Wang, Lincong Zou, Shuxue A New Secondary Structure Assignment Algorithm Using C(α) Backbone Fragments |
title | A New Secondary Structure Assignment Algorithm Using C(α) Backbone Fragments |
title_full | A New Secondary Structure Assignment Algorithm Using C(α) Backbone Fragments |
title_fullStr | A New Secondary Structure Assignment Algorithm Using C(α) Backbone Fragments |
title_full_unstemmed | A New Secondary Structure Assignment Algorithm Using C(α) Backbone Fragments |
title_short | A New Secondary Structure Assignment Algorithm Using C(α) Backbone Fragments |
title_sort | new secondary structure assignment algorithm using c(α) backbone fragments |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813195/ https://www.ncbi.nlm.nih.gov/pubmed/26978354 http://dx.doi.org/10.3390/ijms17030333 |
work_keys_str_mv | AT caochen anewsecondarystructureassignmentalgorithmusingcabackbonefragments AT wangguishen anewsecondarystructureassignmentalgorithmusingcabackbonefragments AT liuan anewsecondarystructureassignmentalgorithmusingcabackbonefragments AT xushutan anewsecondarystructureassignmentalgorithmusingcabackbonefragments AT wanglincong anewsecondarystructureassignmentalgorithmusingcabackbonefragments AT zoushuxue anewsecondarystructureassignmentalgorithmusingcabackbonefragments AT caochen newsecondarystructureassignmentalgorithmusingcabackbonefragments AT wangguishen newsecondarystructureassignmentalgorithmusingcabackbonefragments AT liuan newsecondarystructureassignmentalgorithmusingcabackbonefragments AT xushutan newsecondarystructureassignmentalgorithmusingcabackbonefragments AT wanglincong newsecondarystructureassignmentalgorithmusingcabackbonefragments AT zoushuxue newsecondarystructureassignmentalgorithmusingcabackbonefragments |