Current Bioinformatics - Volume 15, Issue 6, 2020

Background: Apoptosis proteins have a key role in the development and the homeostasis of the organism, and are very important to understand the mechanism of cell proliferation and death. The function of apoptosis protein is closely related to its subcellular location. Objective: Prediction of apoptosis protein subcellular localization is a meaningful task. Methods: In this study, we predict the apoptosis protein subcellular locatio Read More

Background: Lectins are a diverse group of glycoproteins or glycoconjugate proteins that can be extracted from plants, invertebrates and higher animals. Cancerlectins, a kind of lectins, which play a key role in the process of tumor cells interacting with each other and are being employed as therapeutic agents. A full understanding of cancerlectins is significant because it provides a tool for the future direction of cancer therap Read More

Background: Gram-negative bacteria interact with their environment by secreting a wide range of particular substrates (such as proteins) across two lipid bilayers from the cytoplasm to the extracellular space. Determining the types of secreted proteins is beneficial for further research on secreted proteins and secretion systems. Objective: As an essential alternative for experimental methods, an accurate machine learning Read More

Background: Peptibodies, the hybrid of peptides and antibodies, represent a novel strategy in therapeutic use. Previously, we computationally designed an antiangiogenic peptibody PbHRH, which fused the HRH peptide with angiogenesis-suppressing effect and human IgG1 Fc fragment using Romiplostim as template. Molecular modeling and simulation results indicated that it would be a potential drug for the treatment o Read More

Background: Long non-coding RNAs (lncRNAs) are transcripts with a length more than 200 nucleotides, functioning in the regulation of gene expression. More evidence has shown that the biological functions of lncRNAs are intimately related to their subcellular localizations. Therefore, it is very important to confirm the lncRNA subcellular localization. Methods: In this paper, we proposed a novel method to predict the subcell Read More

Background: The non-coding RNA identification at the organelle genome level is a challenging task. In our previous work, an ncRNA dataset with less than 80% sequence identity was built, and a method incorporating an increment of diversity combining with support vector machine method was proposed. Objective: Based on the ncRNA_361 dataset, a novel decision-making method-an improved KNN (iKNN) classifier was pro Read More

Background: Enhancers are cis-regulatory elements that enhance gene expression on DNA sequences. Since most of enhancers are located far from transcription start sites, it is difficult to identify them. As other regulatory elements, the regions around enhancers contain a variety of features, which can help in enhancer recognition. Objective: The classification power of features differs significantly, the performances Read More

Background: The regulatory function of transcription factors on genes is not only related to the location of binding genes and its related functions, but is also related to the methods of binding. Objective: It is necessary to study the regulation effects in different binding methods on target genes. Methods: In this study, we provided a reliable theoretical basis for studying gene expression regulation of co-binding transcription factor Read More

Background: DNA methylation plays an important role in the reprogramming process. Understanding the underlying molecular mechanism of reprogramming is crucial for answering fundamental questions regarding the transition of cell identity. Methods: In this study, based on the genome-wide DNA methylation data from different cell lines, comparative methylation profiles were proposed to identify the epigenetic Read More

A variety of environmental toxicants such as heavy metals, pesticides, organic chemicals, etc produce harmful effects in our living systems. In the literature, various reports have indicated the detrimental effects of toxicants such as immunotoxicity, cardiotoxicity, nephrotoxicity, etc. Experimental animals are generally used to investigate the safety profile of environmental chemicals, but research on animals has som Read More

For two decades, Rosetta has consistently been at the forefront of protein structure prediction. While it has become a very large package comprising programs, scripts, and tools, for different types of macromolecular modelling such as ligand docking, protein-protein docking, protein design, and loop modelling, it started as the implementation of an algorithm for ab initio protein structure prediction. The term ’Rosetta’ Read More

In this brief survey, various aspects of cancer complexity and how this complexity can be confronted using modern complex networks’ theory and gene expression datasets, are described. In particular, the causes and the basic features of cancer complexity, as well as the challenges it brought are underlined, while the importance of gene expression data in cancer research and in reverse engineering of gene co-expression net Read More