Current Bioinformatics - Volume 13, Issue 2, 2018

Background: Biological networks are used to represent interactions involving genes, DNA, RNA and proteins that are able to manipulate many cellular processes. Objective: The aim of this study is to evaluate whether prior knowledge can improve the quality of biological networks, in particular protein-protein interaction networks and gene regulatory networks. Method: Gene Ontology (GO) as well as three different typ Read More

Background: Peptides are chemicals built of 20 types of amino acids linked into long chain called sequence. Determination of amino acid sequence (order) in peptide is a very important issue of modern molecular biology. There is no direct chemical method that allows determining long peptide sequences. The approach to do so is to cut long sequence into short pieces, sequence them and then to figure out what was their order Read More

Background: The ovarian follicle is an essential component of the reproductive process. It plays an important role in controlling the estrous cycle, determining estrous behaviour, ensuring oocyte competency and subsequent embryo survival rate, and determining both post ovulation corpus luteum function and progesterone synthesis. Traditionally, gene expression studies in the field of follicular development focus on the stu Read More

Background: Accumulating studies have indicated that the human microbiome plays critical roles in human health and disease. It is significantly important to analyze the relationships between microbe and disease, which is helpful for the understanding of disease mechanism, diagnosis and therapy. Predicting potential microbe-disease associations would not only boost understanding of the disease mechanism but also it will Read More

Background: Increasing numbers of researchers apply linear B-cell epitope prediction in their research, as in the case of peptide-based vaccine design, diagnostic tests, disease prevention and antibody production. Online software offers major ways of epitope prediction. Objective: With the advent of more and more newly built software, a standard assessment for various prediction tools is urgently needed. Methods: From th Read More

Background: Inhibition of DPP-IV enzyme is an effective strategy for the treatment of type-2 diabetes mellitus, which involves the degradation of incretin hormones, glucagon like peptide (GLP-1) and gastric inhibitory polypeptide (GIP), being valuable in glucose tolerance and insulin secretion. A series of indole alkaloids from the medicinal plant Rauvolfia serpentina were identified as novel DPP-IV inhibitors using insilico predicti Read More

Background: The diagnosis of diseases correctly became a challenge, and any error can cost patients life, especially when there is a lack of knowledge or expertise related to a disease, it often results in patient’s death or takes the form of an epidemic, as we have seen in the case of Ebola. Objective: The automation and the development of reliable diagnostic systems became a necessity. Through the use of technolog Read More

Background: EphrinB2 ligand and its associated receptor have been responsible for mediating signal transduction pathways related to developmental, cell segmentation processes, cell proliferation, etc. Aberrations in ephb2 gene result in altered EPHB2 receptor protein, which in turn, affect the related biological processes. Objective: The objective of this study is to determine the most lethal, non-synonymous SNPs Read More

Background: Protein folding depends on the nature of the amino acid sequence. Once folding process of the amino acid sequence is successful, the protein becomes functional. Recently, a two-dimensional hydrophobic-polar (2D HP) model algorithm has been developed for the effective prediction of protein folding. However, the particular 2D HP models still lack an algorithm for protein folding prediction. Objective: Some Read More

Background: Proteomics was built around two-dimensional (2D) gel electrophoresis. Accurately analyzing the images generated from 2D gel electrophoresis for spot detection is a timeconsuming process especially for high-resolution and large images. Objective: In this paper, we present an accurate GPU-accelerated software tool for the detection and quantification of protein spots in 2D gel electrophoresis images. Metho Read More

Background: Magnolia Bark Extract (MBE), has been utilized in Asia as herbal medicine and a broad range of its potential efficacy was considered such as anti-inflammatory, anti-oxidant, and anti-bacterial. Much interest has been focused on pharmacological actions of two primary active phenolic MBE constituents (magnolol and honokiol). Objective: Our aim is computational studies of the interactions between the bioactiv Read More

Background: Genomes of organisms contains a variety of repeated structures of various lengths and type, interspersed or tandem. Tandem repeats play important role in molecular biology as they are related to genetic backgrounds of inherited diseases, and also they can serve as markers for DNA mapping and DNA fingerprinting. Improving the efficiency of algorithms for searching the tandem repeats in DNA sequences can le Read More