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Int. J. Mol. Sci. 2016, 17(3), 333; doi:10.3390/ijms17030333

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

1,2,†
,
1,2,†
,
3
,
1,2
,
1,2
and
1,2,*
1
College of Computer Science and Technology, Jilin University, Changchun 130012, China
2
Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun 130012, China
3
College of Pharmaceutical Science, Jilin University, Changchun 130012, China
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Christo Z. Christov
Received: 27 January 2016 / Revised: 26 February 2016 / Accepted: 29 February 2016 / Published: 11 March 2016
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
View Full-Text   |   Download PDF [1079 KB, uploaded 11 March 2016]   |  

Abstract

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 Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα 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 (310-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. View Full-Text
Keywords: protein; secondary structure assignment; cluster; Cα backbone fragment; outlier detection protein; secondary structure assignment; cluster; Cα backbone fragment; outlier detection
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Cao, C.; Wang, G.; Liu, A.; Xu, S.; Wang, L.; Zou, S. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments. Int. J. Mol. Sci. 2016, 17, 333.

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