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Protein fold recognition based on functional domain composition ☆

Paper ID Volume ID Publish Year Pages File Format Full-Text
15144 1381 2014 6 PDF Available
Title
Protein fold recognition based on functional domain composition ☆
Abstract

•A method based on functional domain composition to predict protein fold types is proposed.•The result indicates this method is high-performance for protein fold recognition.•LIFCA can reflect the corresponding relation between protein structure and function.

Recognition of protein fold types is an important step in protein structure and function predictions and is also an important method in protein sequence-structure research. Protein fold type reflects the topological pattern of the structure's core. Now there are three methods of protein structure prediction, comparative modeling, fold recognition and de novo prediction. Since comparative modeling is limited by sequence similarity and there is too much workload in de novo prediction, fold recognition has the greatest potential. In order to improve recognition accuracy, a recognition method based on functional domain composition is proposed in this paper. This article focuses on the 124 fold types which have more than 2 samples in LIFCA database. We apply the functional domain composition to predict the fold types of a protein or a domain. In order to evaluate our method and its sensibility to the samples involving SCOP family divided, we tested our results from different aspects. The average sensitivity, specificity and Matthew's correlation coefficient (MCC) of the 124 fold types were found to be 94.58%, 99.96% and 0.91, respectively. Our results indicate that the functional domain composition method is a very promising method for protein fold recognition. And though based on simple classification rules, LIFCA database can grasp the functional features of different proteins, reflecting the corresponding relation between protein structure and function.

Keywords
Functional domain composition; Fold recognition; Fold type; LIFCA database; Protein
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Protein fold recognition based on functional domain composition ☆
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 48, February 2014, Pages 71–76
Authors
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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