The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more t...

Since protein complexes play important biological roles in cells, many computational methods have been proposed to detect protein complexes from protein-protein interaction (PPI) data. In this paper, we first review four reputed protein-complex detection algorithms (MCODE[2], MCL[21], CPA[1] and DECAFF[14]) and then present a comprehensive evaluation among them on two popular yeast PPI data. We...

Abstract Corona virus disease 2019 (COVID-19) is prone to induce multiple organ damage. The kidney one of the target organs SARS-CoV-2, which susceptible inducing acute injury (AKI). Huanglian Jiedu Decoction (HLJDD) recommended prescriptions for COVID-19 with severe complications. We used network pharmacology and molecular docking explore therapeutic protective effects HLJDD on COVID-19-associ...

Background: Endoplasmic reticulum stress (ERS) is involved in the etiology of non-alcoholic fatty liver disease (NAFLD). Thus, current study was designed to identify key ERS-associated genes NAFLD. Methods: RNA-Seq data NAFLD and controls were sourced from Gene Expression Omnibus (GEO) database. Differentially expressed (DEGs) identified by limma. By overlapping DEGs ERS-related genes, identifi...

Proteins are the workhorses of the cell that perform biological functions by interacting with other proteins. Many statistical methods for protein-protein interaction (PPI) have been studied without considering time-dependent changes in networks and the functionalities. I introduced a novel method that models PPI networks as being dynamic in nature and evolving time-varying multivariate distrib...

d/l-Hybrid peptides are an attractive class of molecular modality because they able to exhibit high proteolytic stability and unique structural diversity which cannot be accessed by those consisting only proteinogenic l-amino acids. Despite such expectation, it has not been possible devise de novo d/l-hybrid capable disrupting the function a protein target(s) due lack effective method that reli...

Many studies are aimed at identifying dense clusters/subgraphs from protein-protein interaction (PPI) networks for protein function prediction. However, the prediction performance based on the dense clusters is actually worse than a simple guilt-by-association method using neighbor counting ideas. This indicates that the local topological structures and properties of PPI networks are still open...

Protein-protein interaction (PPI) networks play an important role in studying the functional roles of proteins, including their association with diseases. However, protein interaction networks are not sufficient without the support of additional biological knowledge for proteins such as their molecular functions and biological processes. To complement and enrich PPI networks, we propose to expl...

Although whole-genome sequencing of many organisms has been completed, numerous newly discovered genes are still functionally unknown. Using high-throughput data such as protein-protein interaction (PPI) information to assign putative protein function to the unknown genes has been proposed, since in many cases it is not feasible to annotate the newly discovered genes by sequence-based approache...

Human protein interaction maps have become important tools of biomedical research for the elucidation of molecular mechanisms and the identification of new modulators of disease processes. The Unified Human Interactome database (UniHI, http://www.unihi.org) provides researchers with a comprehensive platform to query and access human protein-protein interaction (PPI) data. Since its first releas...