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Molecular docking and dynamic simulation of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) obtained from Mycobacterium tuberculosis using in silico approach
In this study, the crystal structure of MurB from MTB (PDB Code: 5JZX and resolution of 2.2  Å) bound to FAD and K+ was obtained from Protein Data Bank (PDB). A total of 2157 compounds with the best binding conformations were obtained from the Zinc database through virtual screening. These compounds further screened for drug-likeness, pharmacokinetic properties, physicochemical properties (Lipinski rule of five), and molecular docking analysis to identified ligands with desirable therapeutic properties and good binding energies against MurB. The ligands with the best binding energies were subjected to molecular dynamic (...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - June 2, 2021 Category: Bioinformatics Source Type: research

A hybrid feature selection model based on improved squirrel search algorithm and rank aggregation using fuzzy techniques for biomedical data classification
AbstractFeature selection has gained its importance due to the voluminous nature of the data. Owing to the computational complexity of wrapper approaches, the poor performance of filtering techniques, and the classifier dependency of embedded approaches, hybrid approaches are more commonly used in feature selection. Hybrid approaches use filtering metrics to reduce the computational complexity of wrapper algorithms and are proved to yield better feature subset. Though filtering metrics select the features based on their significance, most of them are unstable and biased towards the metric used. Moreover, the choice of filt...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - June 2, 2021 Category: Bioinformatics Source Type: research

Repurposing natural compounds as potent inhibitors of β-catenin: an integrative in-silico approaches
AbstractNon-small cell lung cancer is one of the hostile diseases among lung cancer diseases and it is mainly due to the presence of cancer stem cells (CSCs). Since CSCs play a crucial role in homeostasis and embryonic development. β-catenin is one of the promising targets in CSC pathways for the development of novel therapeutic agents against NSCLC. Keeping this in mind, an effort was made to unearth novel β-catenin inhibitors from the plant-derived NPACT database which exhibits 1574 compounds. Initially, an e-pharmacophore hypothesis, receptor-cavity-based hypothesis, and shape-based screening were performed based on f...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - June 1, 2021 Category: Bioinformatics Source Type: research

In-silico designing of epitope-based vaccine against the seven banded grouper nervous necrosis virus affecting fish species
In this study we developed an epitope-based vaccine (EBV), against NNV using computation approach. We have selected two conserved proteins RNA-dependent RNA polymerase (RdRP) and capsid proteins. Based on more than  ~ 1000 epitopes we selected six antigenic epitopes. These were conjugated to adjuvant and linker peptides to generate a full-length vaccine candidate. Biochemical structural properties were analyzed by Phyre2 server. ProtParam, Molprobity. Ramachandran plot results indicate that 98.7% residues are in a favorable region and 93.4% residues in the favored region. The engineered EBV binds to toll like receptor-...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - May 31, 2021 Category: Bioinformatics Source Type: research

A study to find a potent feature by combining the various disulphide bonds of protein using data mining technique
AbstractIn the sphere of bioinformatics, the identification of an effective protein feature, is of the essence. The fruitfulness of any classification technique, relies heavily on the identification of informative and distinct features. Various pre-existing classifiers recognised the use of a single type of disulphide bond (viz, parallel, or alternate) as a useful feature. However, the computational efficiency may be increased by the identification of appropriate combination of disulphide bonds, as a single feature. Hence, in this paper, the various combinations of disulphide bonds have been studied, to formulate a potent ...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - May 25, 2021 Category: Bioinformatics Source Type: research

Hybrid image encryption scheme for secure E-health systems
AbstractDNA computing is an area of natural computing inspired by molecular biology. It can be used to perform arithmetic and logic operations on information encoded as DNA strands. Due to the rapid development of network technology, E-health care services are helpful for all patients from anywhere at any time. Patients can use these services through a public channel. The security of patients ’ privacy is therefore an essential issue in E-health care. In this paper, an encryption scheme is proposed for hiding patient information in a medical image using the Least Significant Bit algorithm, which involves hiding data in t...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - May 8, 2021 Category: Bioinformatics Source Type: research

CHD3/4/5/6/8 serve as potential prognostic predictors in human gastric cancer
AbstractChromodomain helicase DNA (CHD) binding protein is one class of chromatin remodeling factors, which are essential in gastric cancer (GC) development. However, the role of distinct CHD family member in GC is rarely understood. To resolve this issue, a comprehensive analysis of the prognostic significance of CHD members in GC was performed using Oncomine, UALCAN, GEPIA, Kaplan –Meier Plotter, cBioPortal, LinkedOmics and STRING databases. The mRNA expression of all CHD members was different in GC samples compared with normal controls, and CHD 1/2/3/6/9 expression was remarkedly correlated with advanced cancer stage....
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - May 5, 2021 Category: Bioinformatics Source Type: research

Swarm optimization-based neural network model for secondary structure prediction of proteins
AbstractProteins form the basis of all major life processes that sustain life. The functionality of a protein is a direct consequence of its underlying structure. Protein structure prediction thus serves to ascertain the function of similar or dissimilar proteins, accordingly. Secondary structure prediction paves way for 3D structures that eventually decides protein properties. It also aims to facilitate probable structures for proteins whose structures remain undiscovered. Although experimental approaches have been quite efficient in extracting protein secondary structure from its amino acid sequence, yet it is often cumb...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 30, 2021 Category: Bioinformatics Source Type: research

Inhibitory effect of anti-HIV compounds extracted from Indian medicinal plants to retard the replication and transcription process of SARS-CoV-2: an insight from molecular docking and MD-simulation studies
In this study, inhibitory efficiency of ten anti-HIV compounds from different Indian medicinal plant parts have been virtually screened against Mpro, PLpro and RdRp proteins of SARS-CoV-2. The molecular docking study reflected that among these compounds, Proptine (PTP) has the highest binding affinity for the three cases. Introduction of PTP molecules within the binding pocket of these proteins showed a large structural and conformational changes on the structure of proteins which is revealed from molecular dynamics (MD) simulation studies. RMSD, RMSF and analysis of thermodynamic parameters also revealed that PTP makes a ...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 30, 2021 Category: Bioinformatics Source Type: research

Guest Editorial: Intelligent solutions for green computing in internet of medical things
(Source: Network Modeling Analysis in Health Informatics and Bioinformatics)
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 26, 2021 Category: Bioinformatics Source Type: research

Exploration of targets and molecular mechanisms of cinnamaldehyde in overcoming fulvestrant-resistant breast cancer: a bioinformatics study
This study aimed to identify the targets and molecular mechanisms of cinnamaldehyde in overcoming fulvestrant-resistant breast cancer using a bioinformatics approach. The microarray data of fulvestrant-resistant and cinnamaldehyde-treated MCF-7 cells were obtained from GSE74391 and GSE85871, respectively, and a total of 310 differentially expressed genes (DEGs) were recovered from these databases. Gene Ontology analysis revealed several DEGs that participated in metabolic processes, responded to a stimulus, were located in the membrane and nucleus, and regulated the molecular functions of the protein and ion binding. Drug ...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 22, 2021 Category: Bioinformatics Source Type: research

A novel enhanced decision tree model for detecting chronic kidney disease
This study uses the recursive feature elimination (RFE) method that selects an optimal subset of features and an ensemble algorithm, the enhanced decision tree (EDT), to predict the disease. The results obtained in this paper show that the accuracy level of EDT is not changed with the removal of less significant features, thus enabling the decision-makers to concentrate on few features to reduce time and error of treatment. EDT establishes substantially high consistency in predicting, with or without feature selection, the disease. (Source: Network Modeling Analysis in Health Informatics and Bioinformatics)
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 11, 2021 Category: Bioinformatics Source Type: research

Binding ability of arginine, citrulline, N -acetyl citrulline and thiocitrulline with SARS COV-2 main protease using molecular docking studies
AbstractIn this article, the binding abilities of arginine, citrulline,N-acetyl citrulline and thiocitrulline on the active sites of SARS-COV-2 protease have been investigated using in-silico studies. All the above ligands bind selectively and preferentially to Cys-145 active site and also to other amino acids surrounding to it in the main protease. Of which arginine forms less number of weaker bonds compared to the other ligands, it by itself is a precursor for the formation of citrulline analogues with in the cell. Major advantage of using the above ligands is that in addition to its preferential binding, they have the a...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 6, 2021 Category: Bioinformatics Source Type: research

Unveiling ancestral relations, host –pathogen interactions and comparative viral miRNA insights of dengue virus serotypes
This study can facilitate one stepping stone in the development and production of preventive, affordable, and safe antiviral medications. (Source: Network Modeling Analysis in Health Informatics and Bioinformatics)
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 5, 2021 Category: Bioinformatics Source Type: research

Telehealth and the digital divide as a social determinant of health during the COVID-19 pandemic
AbstractTelehealth has been shown to have comparable health outcomes in terms of patient-physician communication, and patient satisfaction and engagement. Nevertheless, the digital divide has exacerbated the social and economic factors that create barriers to health and well-being. It, therefore, maybe a social determinant of health (SDOH). Such issues as decreased internet connectivity and a lack of Wi-Fi and video chat/webcam in both urban and rural areas can hinder the effectiveness of telehealth to its full capability, especially among communities of color, the poor, and medically underserved. The social aspects of the...
Source: Network Modeling Analysis in Health Informatics and Bioinformatics - April 3, 2021 Category: Bioinformatics Source Type: research