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Protein amino acid solvent exposure plays a crucial role in understanding, analyzing and predicting protein structure and function. In this paper, we propose a novel three-dimensional measure of solvent exposure named Eighth-Sphere Exposure based on three-dimensional protein structures. This measure supposes a sphere with a radius of 13Å around a Cα atom, and subdivides its microenvironment into...
In some real-world applications, the predefined features are not discriminative enough to represent well the distinctiveness of different classes. Therefore, building a more well-defined feature space becomes an urgent task. The main goal of feature space transformation is to map a set of features defined in a space into a new more powerful feature space so that the classification based on the transformed...
Identification of salient patterns for the classification of gene expression profiles is a useful step in examining the biological significance and correlation of genes with disease states. We propose a clustering-based approach in which feature selection is first carried out to identify influential genes and then salient patterns are determined to characterize each of the different classes. The proposed...
Heart disease is the one of the significant health problem in the world. Recently, most serious problem caused by it is that the patient becomes younger. Therefore, it is very important and necessary to find the early symptoms of heart problems for better treatment and effective methodology for predicting the disease. Data mining is the one of the efficient approaches. However, there are still some...
It is well known that amino acids in peptides and proteins show individually distinct preferences for secondary structural conformations. While each amino acid is associated with multiple physicochemical properties, most existing statistical analysis methods treat amino acids separately and independently in calculating the frequencies of residues at each site of protein sequences. Such approaches...
As evidenced by a buried core of hydrophobic residues within globular proteins, hydrophobicity provides essential insights into the folding structure of proteins. Previous studies have shown that hydrophobic residues show statistically meaningful distribution on the primary sequence, but most of them lacked further investigation into a potential relationship to secondary structure elements. In this...
Eight representative physicochemical properties of amino acids are considered to encode each residue and correlative information is examined in relation to the formation of protein secondary structure. Features salient at the coarse level are first gleaned through vector quantization technique and then more refined class-specific features are identified based on the vector element-wise analysis. Effectiveness...
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