Current Bioinformatics - Volume 15, Issue 4, 2020

Molecular Docking is used to positioning the computer-generated 3D structure of small ligands into a receptor structure in a variety of orientations, conformations and positions. This method is useful in drug discovery and medicinal chemistry providing insights into molecular recognition. Docking has become an integral part of Computer-Aided Drug Design and Discovery (CADDD). Traditional docking methods suffer from limitation Read More

Background: Pseudouridine (Ψ) is the most abundant RNA modification and has important functions in a series of biological and cellular processes. Although experimental techniques have made great contributions to identify Ψ sites, they are still labor-intensive and costineffective. In the past few years, a series of computational approaches have been developed, which provided rapid and efficient approaches to identify Ψ sites Read More

Background: The brain networks can provide us an effective way to analyze brain function and brain disease detection. In brain networks, there exist some import neural unit modules, which contain meaningful biological insights. Objective: Therefore, we need to find the optimal neural unit modules effectively and efficiently. Method: In this study, we propose a novel algorithm to find community modules of brain networks by Read More

Background: Protein phosphorylation is one of the most important Post-translational Modifications (PTMs) occurring at amino acid residues serine (S), threonine (T), and tyrosine (Y). It plays critical roles in protein structure and function predicting. With the development of novel high-throughput sequencing technologies, there are a huge amount of protein sequences being generated and stored in databases. Objective: It is of gre Read More

Background: Ensemble building is a popular method for improving model accuracy for classification problems as well as regression. Objective: In this research work, we propose a sequential ensemble model to predict the number of incidences for communicable diseases like influenza, hand foot and mouth disease (HFMD), and diarrhea and compare it with applied models for prediction. Methods: The weekly dataset of the thr Read More

Background: The rapidly growing protein and annotation databases necessitate the development of efficient tools to process this valuable information. Biologists frequently need to find proteins similar to a given protein, for which BLAST tools are commonly used. With the development of biomedical ontologies, e.g. Gene Ontology, methods were designed to measure function (semantic) similarity between two proteins. T Read More

Background: Oral Squamous Cell Carcinoma (OSCC) is the most common malignant epithelial neoplasm. It is located within the top 10 ranking incidence of cancers with a poor prognosis and low survival rates. New breakthroughs of therapeutic strategies are therefore needed to improve the survival rate of OSCC harboring patients. Objective: Since targeted therapy is considered as the most promising therapeutic strategi Read More

Background: Molecular biomarkers show new ways to understand many disease processes. Noncoding RNAs as biomarkers play a crucial role in several cellular activities, which are highly correlated to many human diseases especially cancer. The classification and the identification of ncRNAs have become a critical issue due to their application, such as biomarkers in many human diseases. Objective: Most existing computation Read More

Background: Ultrasound test is one of the routine tests for the diagnosis of thyroid cancer. The diagnosis accuracy depends largely on the correct interpretation of ultrasound images of thyroid nodules. However, human eye-based image recognition is usually subjective and sometimes error-prone especially for less experienced doctors, which presents a need for computeraided diagnostic systems. Objective: To our best know Read More

Background: Non-negative Matrix Factorization (NMF) has been extensively used in gene expression data. However, most NMF-based methods have single-layer structures, which may achieve poor performance for complex data. Deep learning, with its carefully designed hierarchical structure, has shown significant advantages in learning data features. Objective: In bioinformatics, on the one hand, to discover differentially expre Read More

Background/Objective: Protein-protein interactions are essentials for most cellular processes and thus, unveiling how proteins interact with is a crucial question that can be better understood by recognizing which residues participate in the interaction. Although many computational approaches have been proposed to predict interface residues, their feature perspective and model learning ability are not enough to ac Read More