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Title

Prediction of temperature factors from protein sequence

 

Authors

Shrihari Sonavane1*, Ashok A Jaybhaye2 & Ajaykumar G Jadhav1

 

Affiliation

1Department of Microbiology, Institute of Science, Caves Roed, Aurangabad, India-431004; 2Maharashtra Hybrid Seeds Company Limited Jalna-Aurangabad Rd, Jalna, India-431004

 

Email

shriharry@gmail.com; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received January 06, 2013; Accepted January 10, 2013; Published February 06, 2013

 

Abstract

Protein flexibility is useful in structural and functional aspect of proteins. We have analyzed the local primary protein sequence features that in combination can predict the B-value of amino acid residues directly from the protein sequence. We have also analyzed the distribution of B-value in different regions of protein three dimensional structures. On an average, the normalized B-value decreases by 0.1055 with every 0.5 increase in the distance of the residue from protein surface. The residues in the loop regions have higher B-values as compared to the residues present in other regular secondary structural elements. Buried residues which are present in the protein core are more rigid (lower B-values) than the residues present on the protein surface. Similarly, the hydrophobic residues which tend to be present in the protein core have lower average B-value than the polar residues. Finally, we have proposed the method based on Support Vector Regression (SVR) to predict the B-value from protein primary sequence. Our result shows that, the SVR model achieved the correlation coefficient of 0.47 which is comparable to existing methods.

 

Keywords

B-value, Protein flexibility, Support Vector Regression, Sliding window approach, Protein dynamics.

 

Citation

Sonavane et al Bioinformation 9(3): 134-140 (2013)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.