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Prediction of temperature factors from protein sequence.

Sonavane S, Jaybhaye AA, Jadhav AG - Bioinformation (2013)

Bottom Line: On an average, the normalized Bvalue decreases by 0.1055 with every 0.5Å 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.Our result shows that, the SVR model achieved the correlation coefficient of 0.47 which is comparable to existing methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Institute of Science, Caves Roed, Aurangabad, India-431004.

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 Bvalue decreases by 0.1055 with every 0.5Å 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.

No MeSH data available.


Related in: MedlinePlus

Frequency distribution of normalized B-value in polarcharged, polar uncharged and non polar hydrophobic aminoacids.
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Related In: Results  -  Collection


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Figure 3: Frequency distribution of normalized B-value in polarcharged, polar uncharged and non polar hydrophobic aminoacids.

Mentions: Amino acids on the basis of their biochemical characteristics aredivided into 3 types as polar charged, polar uncharged and nonpolar hydrophobic amino acids. The frequency distribution ofnormalized B-values for each type is shown in (Figure 3). Thedistribution of normalized B-value in polar uncharged residuesis similar to that of the overall distribution in the dataset, whilethe distribution of normalized B-value in non polarhydrophobic and polar charged is similar to the one in buriedand intermediate surface residues, respectively.


Prediction of temperature factors from protein sequence.

Sonavane S, Jaybhaye AA, Jadhav AG - Bioinformation (2013)

Frequency distribution of normalized B-value in polarcharged, polar uncharged and non polar hydrophobic aminoacids.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3569600&req=5

Figure 3: Frequency distribution of normalized B-value in polarcharged, polar uncharged and non polar hydrophobic aminoacids.
Mentions: Amino acids on the basis of their biochemical characteristics aredivided into 3 types as polar charged, polar uncharged and nonpolar hydrophobic amino acids. The frequency distribution ofnormalized B-values for each type is shown in (Figure 3). Thedistribution of normalized B-value in polar uncharged residuesis similar to that of the overall distribution in the dataset, whilethe distribution of normalized B-value in non polarhydrophobic and polar charged is similar to the one in buriedand intermediate surface residues, respectively.

Bottom Line: On an average, the normalized Bvalue decreases by 0.1055 with every 0.5Å 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.Our result shows that, the SVR model achieved the correlation coefficient of 0.47 which is comparable to existing methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Institute of Science, Caves Roed, Aurangabad, India-431004.

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 Bvalue decreases by 0.1055 with every 0.5Å 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.

No MeSH data available.


Related in: MedlinePlus