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This article presents a new SVM classifier for the prediction of the extended early-stage (ES) protein structures. The classifier is based on physicochemical features and position-specific scoring matrix (PSSM). Experiments have shown that prediction results for specific classes are significantly better than those already obtained.
Protein-protein interactions (PPI) occur at every level of cell functions. The identification of protein interactions provides a global picture of cellular functions and biological processes. It is also an essential step in the construction of PPI networks for human and other organisms. PPI prediction has been considered a promising alternative to the traditional drug design techniques. The identification...
Using graph databases becomes increasingly popular in domains where data can be modeled as a set of connected objects. Graph databases enable to query such data using graphbased queries in a relatively simple manner in comparison to the classical relational databases. In this paper, we show how one of the most popular graph databases, Neo4j, can be applied to the bioinformatics problem of protein-protein...
Immune algorithm is a rising algorithm which simulates the organism immune system by computer. One of the immune algorithms named clonal selection algorithm is widely used due to its adaptability, implicit parallelism and diversity. A fitness function is constructed in this paper by using protein folding restrictions, such as amino acids' hydrophobicity rule, protein's secondary structure folding...
Due to the enormous amount of data in DNA sequences to be processed, the computational complexity and speed are important issues to be considered. In this paper, a new integrative method is presented for predicting protein coding regions. We first establish a Takagi-Sugeno fuzzy model to identify the first nucleotide of a codon in coding regions, then the time-frequency characteristics of the output...
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