Current Bioinformatics - Volume 14, Issue 3, 2019

Background: Protein inter-residue contacts prediction play an important role in the field of protein structure and function research. As a low-dimensional representation of protein tertiary structure, protein inter-residue contacts could greatly help de novo protein structure prediction methods to reduce the conformational search space. Over the past two decades, various methods have been developed for protein inte Read More

Background: Proteins play a crucial role in life activities, such as catalyzing metabolic reactions, DNA replication, responding to stimuli, etc. Identification of protein structures and functions are critical for both basic research and applications. Because the traditional experiments for studying the structures and functions of proteins are expensive and time consuming, computational approaches are highly desired. In ke Read More

Background: Traditional Chinese Medicine (TCM) is widely utilized as complementary health care in China whose acceptance is still hindered by conventional scientific research methodology, although it has been exercised and implemented for nearly 2000 years. Identifying the molecular mechanisms, targets and bioactive components in TCM is a critical step in the modernization of TCM because of the complexity and uniq Read More

Background: Essential proteins play important roles in the survival or reproduction of an organism and support the stability of the system. Essential proteins are the minimum set of proteins absolutely required to maintain a living cell. The identification of essential proteins is a very important topic not only for a better comprehension of the minimal requirements for cellular life, but also for a more efficient discovery of the hu Read More

Background: B-cell epitope prediction is an essential tool for a variety of immunological studies. For identifying such epitopes, several computational predictors have been proposed in the past 10 years. Objective: In this review, we summarized the representative computational approaches developed for the identification of linear B-cell epitopes. Methods: We mainly discuss the datasets, feature extraction metho Read More

Background: The location of proteins in a cell can provide important clues to their functions in various biological processes. Thus, the application of machine learning method in the prediction of protein subcellular localization has become a hotspot in bioinformatics. As one of key organelles, the Golgi apparatus is in charge of protein storage, package, and distribution. Objective: The identification of protein location in Golgi appar Read More

Background: Studies have shown that exogenous miRNAs have cross-kingdom regulatory effects on bacteria and viruses, but whether exogenous plant miRNAs are stable in human body or participate in cross-kingdom regulation is still controversial. Objective: This study aims to propose a new method for the presence and cross-kingdom regulation pathway of exogenous Plant miRNA, which combines biological calculations and Read More

Background: DNA-binding proteins, binding to DNA, widely exist in living cells, participating in many cell activities. They can participate some DNA-related cell activities, for instance DNA replication, transcription, recombination, and DNA repair. Objective: Given the importance of DNA-binding proteins, studies for predicting the DNA-binding proteins have been a popular issue over the past decades. In this article, we review curr Read More

Background: Gene Regulatory Network (GRN) inference algorithms aim to explore casual interactions between genes and transcriptional factors. High-throughput transcriptomics data including DNA microarray and single cell expression data contain complementary information in network inference. Objective: To enhance GRN inference, data integration across various types of expression data becomes an economic and effi Read More

Background: Accumulating experimental studies have manifested that long-non-coding RNAs (lncRNAs) play an important part in various biological process. It has been shown that their alterations and dysregulations are closely related to many critical complex diseases. Objective: It is of great importance to develop effective computational models for predicting potential lncRNA-disease associations. Method: Based on the hypot Read More