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PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive Cα atoms ☆

Paper ID Volume ID Publish Year Pages File Format Full-Text
15363 1407 2008 6 PDF Available
Title
PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive Cα atoms ☆
Abstract

The automatic assignment of secondary structure from three-dimensional atomic coordinates of proteins is an essential step for the analysis and modeling of protein structures. So different methods based on different criteria have been designed to perform this task. We introduce a new method for protein secondary structure assignment based solely on Cα coordinates. We introduce four certain relations between Cα three-dimensional coordinates of consecutive residues, each of which applies to one of the four regular secondary structure categories: α-helix, 310-helix, π-helix and β-strand. In our approach, the deviation of the Cα coordinates of each residue from each relation is calculated. Based on these deviation values, secondary structures are assigned to all residues of a protein. We show that our method agrees well with popular methods as DSSP, STRIDE and assignments in PDB files. It is shown that our method gives more information about helix geometry leading to more accurate secondary structure assignment.

Keywords
Regular secondary structure; Protein secondary structure assignment; Cα three-dimensional coordinates
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PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive Cα atoms ☆
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 32, Issue 6, December 2008, Pages 406–411
Authors
, , , , ,
Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
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Any Questions? feel free to contact us