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Inter-domain linker prediction using amino acid compositional index

Paper ID Volume ID Publish Year Pages File Format Full-Text
15043 1369 2015 8 PDF Available
Title
Inter-domain linker prediction using amino acid compositional index
Abstract

•We developed a domain linker predictor from amino acid sequence information.•A modified formula for amino acid compositional index is proposed.•Domain-linker regions are identified using the amino acid compositional index.•A simulated annealing algorithm is employed and tuned to enhance the prediction.•The method showed a significant improvement over current methods.

Protein chains are generally long and consist of multiple domains. Domains are distinct structural units of a protein that can evolve and function independently. The accurate and reliable prediction of protein domain linkers and boundaries is often considered to be the initial step of protein tertiary structure and function predictions. In this paper, we introduce CISA as a method for predicting inter-domain linker regions solely from the amino acid sequence information. The method first computes the amino acid compositional index from the protein sequence dataset of domain-linker segments and the amino acid composition. A preference profile is then generated by calculating the average compositional index values along the amino acid sequence using a sliding window. Finally, the protein sequence is segmented into intervals and a simulated annealing algorithm is employed to enhance the prediction by finding the optimal threshold value for each segment that separates domains from inter-domain linkers. The method was tested on two standard protein datasets and showed considerable improvement over the state-of-the-art domain linker prediction methods.

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Keywords
Domain linker prediction; Amino acid composition; Compositional index; Simulated annealing
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Inter-domain linker prediction using amino acid compositional index
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 55, April 2015, Pages 23–30
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
Online Support
Any Questions? feel free to contact us