An Across-Target Study on Visual Attentions in Facial Expression Recognition
AbstractAs a simulation of human expression recognition, the studies on automatic expression recognition expect to draw useful enlightenment through close, accurate observation on human expression processing via advanced devices. Eye-trackers are mostly used devices that are technically designed to obtain eye-movement data. However, due to the discrepancy between target faces, across-target analysis is limited in these studies, and this much reduces the chance of finding the latent eye-behavior patterns. Through the utilization of correspondences between targets, this study achieves an across-target analysis to explore the...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 30, 2018 Category: Bioinformatics Source Type: research

Risk-Predicting Model for Incident of Essential Hypertension Based on Environmental and Genetic Factors with Support Vector Machine
In conclusion, the model based on SVM with Laplacian kernel function had better performance in predicting risk of hypertension. And SVM model considering both environmental and genetic factors had better performance than the model with environmental or genetic factors onl y. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - January 29, 2018 Category: Bioinformatics Source Type: research

An Ensemble Framework Coping with Instability in the Gene Selection Process
AbstractThis paper proposes an ensemble framework for gene selection, which is aimed at addressing instability problems presented in the gene filtering task. The complex process of gene selection from gene expression data faces different instability problems from the informative gene subsets found by different filter methods. This makes the identification of significant genes by the experts difficult. The instability of results can come from filter methods, gene classifier methods, different datasets of the same disease and multiple valid groups of biomarkers. Even though there is a wide number of proposals, the complexity...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 8, 2018 Category: Bioinformatics Source Type: research

Detoxification of aflatoxins on prospective approach: effect on structural, mechanical, and optical properties under pressures
AbstractAflatoxins are sequential of derivatives of coumarin and dihydrofuran with similar chemical structures and well-known carcinogenic agent. Many studies performed to detoxify aflatoxins, but the result is not ideal. Therefore, we studied structural, infrared spectrum, mechanical, and optical properties of these compounds in the aim of perspective physics. Mulliken charge distributions and infrared spectral analysis performed to understand the structural difference between the basic types of aflatoxins. In addition, the effect of pressure, different polarized, and incident directions on their structural changes was de...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 27, 2017 Category: Bioinformatics Source Type: research

visnormsc: A Graphical User Interface to Normalize Single-cell RNA Sequencing Data
AbstractSingle-cell RNA sequencing (RNA-seq) allows the analysis of gene expression with high resolution. The intrinsic defects of this promising technology imports technical noise into the single-cell RNA-seq data, increasing the difficulty of accurate downstream inference. Normalization is a crucial step in single-cell RNA-seq data pre-processing. SCnorm is an accurate and efficient method that can be used for this purpose. An R implementation of this method is currently available. On one hand, the R package possesses many excellent features from R. On the other hand, R programming ability is required, which prevents the...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 26, 2017 Category: Bioinformatics Source Type: research

Modeling and Control of a Delayed Hepatitis B Virus Model with Incubation Period and Combination Treatment
AbstractIn this paper, a hepatitis B virus (HBV) model with an incubation period and delayed state and control variables is firstly proposed. Furthermore, the combination treatment is adopted to have a longer-lasting effect than mono-therapy. The equilibrium points and basic reproduction number are calculated, and then the local stability is analyzed on this model. We then present optimal control strategies based on the Pontryagin ’s minimum principle with an objective function not only to reduce the levels of exposed cells, infected cells and free viruses nearly to zero at the end of therapy, but also to minimize th...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 19, 2017 Category: Bioinformatics Source Type: research

Genome-Wide Assessment of Polygalacturonases-Like (PGL) Genes of Medicago truncatula , Sorghum bicolor , Vitis vinifera and Oryza sativa Using Comparative Genomics Approach
AbstractThe polygalacturonases (PG) is one of the important members of pectin-degrading glycoside hydrolases of the family GH28. In plants, PG represents multigene families associated with diverse processes. In the present study, an attempt has been made to investigate the diversity of PG genes among monocots and dicots with respect to phylogeny, gene duplication and subcellular localization to get an insight into the evolutionary and functional attributes. The genome-wide assessment ofMedicago truncatula,Vitis vinifera Sorghum bicolor, andOryza sativa L. ssp.japonica genomes revealed 53, 49, 38 and 35 PG-like (PGL) gen...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 14, 2017 Category: Bioinformatics Source Type: research

Neural Network Modeling of AChE Inhibition by New Carbazole-Bearing Oxazolones
AbstractAcetylcholine esterase (AChE) is one of the targeted enzymes in the therapy of important neurodegenerative diseases such as Alzheimer ’s disease. Many studies on carbazole- and oxazolone-based compounds have been conducted in the last decade due to the importance of these compounds. New carbazole-bearing oxazolones were synthesized from several carbazole aldehydes and p-nitrobenzoyl glycine as AChE inhibitors by the Erlenmeyer r eaction in the present study. The inhibitory effects of three carbazole-bearing oxazolone derivatives on AChE were studied in vitro and the experimental results were modeled using art...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 13, 2017 Category: Bioinformatics Source Type: research

Structural Probing, Screening and Structure-Based Drug Repositioning Insights into the Identification of Potential Cox-2 Inhibitors from Selective Coxibs
AbstractThe rate-limiting enzyme cyclooxygenase-2 (COX-2) is considered as an insightful prognostic target for non-small cell lung cancer (NSCLC) therapy. Now, administration and prolonged utilization of selective COX-2 inhibitors (COXIBs) towards moderating the NSCLC has been associated with different side effects. In the present study, we focused on the structure-based drug repositioning approaches for predicting therapeutic potential de novo candidates for human COX-2. Due to discrepancies in the eminence of x-ray diffraction structures, creates a big barrier in drug discovery approach. Hence, the adaptable COX-2 struct...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 13, 2017 Category: Bioinformatics Source Type: research

Comparing Reverse Complementary Genomic Words Based on Their Distance Distributions and Frequencies
This study uses both the complete human genome and its repeat-masked version. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - December 6, 2017 Category: Bioinformatics Source Type: research

Inferring Gene Regulatory Networks Based on a Hybrid Parallel Genetic Algorithm and the Threshold Restriction Method
AbstractInferring gene regulatory networks (GRNs) is a challenging computational task in system biology. Many inference algorithms have been proposed along with related modifications to various problems. Every algorithm has its own advantages and drawbacks. In particular, the efficiency of each algorithm is not as good as people expect. A novel inference algorithm is proposed in this paper that can be divided into two parts. In the first part, the pre-computational part, two tasks must be accomplished: singular value decomposition for solution space determination and the threshold restriction method for redundant edge dele...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 4, 2017 Category: Bioinformatics Source Type: research

Identification of Disease Critical Genes Using Collective Meta-heuristic Approaches: An Application to Preeclampsia
AbstractIdentifying a small subset of disease critical genes out of a large size of microarray gene expression data is a challenge in computational life sciences. This paper has applied four meta-heuristic algorithms, namely, honey bee mating optimization (HBMO), harmony search (HS), differential evolution (DE) and genetic algorithm (basic version GA) to find disease critical genes of preeclampsia which affects women during gestation. Two hybrid algorithms, namely, HBMO-kNN and HS-kNN have been newly proposed here where kNN (k nearest neighbor classifier) is used for sample classification. Performances of these new approac...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 1, 2017 Category: Bioinformatics Source Type: research

Association of Inflammatory Bowel Disease with Arthritis: Evidence from In Silico Gene Expression Patterns and Network Topological Analysis
This study also suggests that TMTC1, INBHA, TMEM45A and SAMD9L DEGs and their accompanying pathways might have the potential to be exploited as drug targets and biomarkers in the diagnosis and/or treatment of IBD linked arthritis and warrants for further experimental va lidation. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - November 17, 2017 Category: Bioinformatics Source Type: research

Distinguishing the disease-associated SNPs based on composition frequency analysis
AbstractSingle-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process. Therefore, it is important to distinguish dSNPs from the usual SNPs. Analysis here show...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 16, 2017 Category: Bioinformatics Source Type: research

Genome-Wide Prediction of Potential Vaccine Candidates for Campylobacter jejuni Using Reverse Vaccinology
AbstractCampylobacteriosis is a deadly disease which has developed resistance to most of the available chemotherapeutic agents. Although various studies provide evidence of acquired immunity following exposure toCampylobacter jejuni, no effective vaccine has been developed, still. Hence, there is an urgent need to identify potential vaccine candidates forCampylobacter species. In the proposed study,Campylobacter jejuni subsp.jejuni serotype O:2 (strain NCTC 11168) was taken and computational approach was employed to screenC. jejuni genome for promising vaccine candidates. From 1623 protein-coding sequences, 37 potential an...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 11, 2017 Category: Bioinformatics Source Type: research

A Novel Hypergraph-Based Genetic Algorithm (HGGA) Built on Unimodular and Anti-homomorphism Properties for DNA Sequencing by Hybridization
AbstractThe sequencing by hybridization (SBH) of determining the order in which nucleotides should occur on a DNA string is still under discussion for enhancements on computational intelligence although the next generation of DNA sequencing has come into existence. In the last decade, many works related to graph theory-based DNA sequencing have been carried out in the literature. This paper proposes a method for SBH by integrating hypergraph with genetic algorithm (HGGA) for designing a novel analytic technique to obtain DNA sequence from its spectrum. The paper represents elements of the spectrum and its relation as hyper...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 6, 2017 Category: Bioinformatics Source Type: research

In Silico Evaluation of Variable pH on the Binding of Epidermal Growth Factor Receptor Ectodomain to its Ligand Through Molecular Dynamics Simulation in Tumors
AbstractMany aggressive and metastatic cancer cell types show Warburg Effect; therefore, it is a possible adaptation helping cancer cells to rapidly divide and utilize the glycolytic intermediates for biosynthesis of ribose sugars (for nucleotide biosynthesis), fatty acid synthesis (lipids for membrane synthesis), NADPH (cellular currency for reductive biosynthesis) and lactate. This in due course results in decrease of extracellular pH, leading to acidic tumor micro-environment. EGFR is a crucial cell surface signaling receptor implicated in cancer cell survival and progression. This warrants studying the effect of the ac...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 4, 2017 Category: Bioinformatics Source Type: research

A Comprehensive Computational Analysis of Mycobacterium Genomes Pinpoints the Genes Co-occurring with YczE, a Membrane Protein Coding Gene Under the Putative Control of a MocR, and Predicts its Function
AbstractBacterial proteins belonging to the YczE family are predicted to be membrane proteins of yet unknown function. In many bacterial species, theyczE gene coding for the YczE protein is divergently transcribed with respect to an adjacent transcriptional regulator of the MocR family. According to in silico predictions, proteins named YczR are supposed to regulate the expression ofyczE genes. These regulators linked to theyczE genes are predicted to constitute a subfamily within the MocR family. To put forward hypotheses amenable to experimental testing about the possible function of the YczE proteins, a phylogenetic pro...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 2, 2017 Category: Bioinformatics Source Type: research

An Innovative Framework for Bioimage Annotation and Studies
AbstractThe collection and analysis of clinical data are needed to investigate diseases and to define medical protocols and treatments. Bioimages, medical annotations and patient history are clinical data acquired and studied to perform a correct diagnosis and to propose an appropriate therapy. Currently, hospital departments manage these data using legacy systems which do not often allow data integration among different departments or health structures. Thus, in many cases clinical information sharing and exchange are difficult to implement. This is also the case for biomedical images for which data integration or data ov...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 1, 2017 Category: Bioinformatics Source Type: research

Discovery of T-cell Driven Subunit Vaccines from Zika Virus Genome: An Immunoinformatics Approach
AbstractThe recent outbreaks of Zika virus and the absence of a specific therapy have necessitated to identify T-cell-stimulating antigenic peptides as potential subunit vaccine candidates. The translated ssRNA (+) genome of Zika virus was explored in EMBOSS antigenic and VaxiJen to predict 63 peptides as potential antigens. Three MHC-II binding peptide prediction tools, viz. NetMHCIIpan, PREDIVAC and immune epitope database (IEDB) were employed in consensus on 63 antigenic peptides to propose 14 T-helper cell epitopes. Similarly, analysis on 63 antigenic peptides through NetMHC, NetCTL and IEDB MHC-I binding peptide predi...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 1, 2017 Category: Bioinformatics Source Type: research

Rare Diseases: Drug Discovery and Informatics Resource
AbstractA rare disease refers to any disease with very low prevalence individually. Although the impacted population is small for a single disease, more than 6000 rare diseases affect millions of people across the world. Due to the small market size, high cost and possibly low return on investment, only in recent years, the research and development of rare disease drugs have gradually risen globally, in several domains including gene therapy, enzyme replacement therapy, and drug repositioning. Due to the complex etiology and heterogeneous symptoms, there is a large gap between basic research and patient unmet needs for rar...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 1, 2017 Category: Bioinformatics Source Type: research

Insight into a Transcriptional Adaptor Zinc Finger Encoded by a Putative Protein in the White Spot Syndrome Virus Genome
AbstractThe transcriptional adaptor zinc (TAZ) fingers are a specialized class of zinc finger domains reported to exist only in eukaryotic transcriptional coactivator proteins. A putative protein within the shrimp white spot syndrome virus (WSSV) encodes for a TAZ domain, which is unique as no virus so far has been reported for the presence of this domain. Our study shows the viral TAZ domain to be similar to TAZ2 rather than TAZ1 domain of eukaryotic CREB-binding proteins and its paralog p300 proteins. Furthermore, as with eukaryotic TAZ2 domain which interacts and binds to several transcriptional factors including the p5...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 31, 2017 Category: Bioinformatics Source Type: research

Survey on Monitoring and Quality Controlling of the Mobile Biosignal Delivery
AbstractA Mobile Patient Monitoring System (MPMS) acquires patient ’s biosignals and transmits them using wireless network connection to the decision-making module or healthcare professional for the assessment of patient’s condition. A variety of wireless network technologies such as wireless personal area networks (e.g., Bluetooth), mobile ad-hoc networks (MAN ET), and infrastructure-based networks (e.g., WLAN and cellular networks) are in practice for biosignals delivery. The wireless network quality-of-service (QoS) requirements of biosignals delivery are mainly specified in terms of required bandwidth, acce...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 31, 2017 Category: Bioinformatics Source Type: research

Identification of Ideal Multi-targeting Bioactive Compounds Against Mur Ligases of Enterobacter aerogenes and Its Binding Mechanism in Comparison with Chemical Inhibitors
AbstractEnterobacter aerogenes have been reported as important opportunistic and multi-resistant bacterial pathogens for humans during the last three decades in hospital wards. The emergence of drug-resistantE. aerogenes demands the need for developing new drugs. Peptidoglycan is an important component of the cell wall of bacteria and the peptidoglycan biochemical pathway is considered as the best source of antibacterial targets. Within this pathway, four Mur ligases MurC, MurD, MurE, and MurF are responsible for the successive additions ofl-alanine and suitable targets for developing novel antibacterial drugs. As an infer...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 31, 2017 Category: Bioinformatics Source Type: research

Diversity in αβ and βα Loop Connections in TIM Barrel Proteins: Implications for Stability and Design of the Fold
In this study, αβ and βα loops from a data set of 430 non-redundant, high-resolution triosephosphate isomerase (TIM) barrels bearing sequence homology of
Source: Interdisciplinary Sciences, Computational Life Sciences - October 24, 2017 Category: Bioinformatics Source Type: research

Common Subcluster Mining in Microarray Data for Molecular Biomarker Discovery
AbstractMolecular biomarkers can be potential facilitators for detection of cancer at early stage which is otherwise difficult through conventional biomarkers. Gene expression data from microarray experiments on both normal and diseased cell samples provide enormous scope to explore genetic relations of disease using computational techniques. Varied patterns of expressions of thousands of genes at different cell conditions along with inherent experimental error make the task of isolating disease related genes challenging. In this paper, we present a data mining method, common subcluster mining (CSM), to discover highly per...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 11, 2017 Category: Bioinformatics Source Type: research

Genome-Wide Analysis of Microsatellites in Alternaria arborescens and Elucidation of the Function of Polyketide Synthase (PksJ)
AbstractMicrosatellites or simple sequence repeats (SSRs) have been the most widely applied class of molecular markers used in genetic studies, having applications in genetic conservation, population studies, as well as diagnostics of fungi. Mining and analysis of SSRs of the whole genome sequence have been carried out in this study for the fungusAlternaria arborescens causing early blight of tomato and well known for producing mycotoxins like alternariol (AOH), alternariol monomethyl ether (AME), etc. A total of 4097 microsatellites were identified inA. Arborescens genome. Contig 1 was identified as the most SSR-rich regi...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 3, 2017 Category: Bioinformatics Source Type: research

Accelerating Biomedical Signal Processing Using GPU: A Case Study of Snore Sound Feature Extraction
AbstractThe advent of ‘Big Data’ and ‘Deep Learning’ offers both, a great challenge and a huge opportunity for personalised health-care. In machine learning-based biomedical data analysis, feature extraction is a key step for ‘feeding’ the subsequent classifiers. With increasing numbers of biomedical data, ex tracting features from these ‘big’ data is an intensive and time-consuming task. In this case study, we employ a Graphics Processing Unit (GPU) via Python to extract features from a large corpus of snore sound data. Those features can subsequently be imported into many w...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 25, 2017 Category: Bioinformatics Source Type: research

Identification of a New Isoindole-2-yl Scaffold as a Qo and Qi Dual Inhibitor of Cytochrome bc 1 Complex: Virtual Screening, Synthesis, and Biochemical Assay
In this study, a virtual screening of NCI diversity database was carried out in order to find novel Qo/Qi cytbc1 complex inhibitors. Structure-based virtual screening and molecular docking methodology were employed to further screen compounds with inhibition activity against cytbc1 complex after extensive reliability validation protocol with cross-docking method and identification of the best score functions. Subsequently, the application of rational filtering procedure over the target database resulted in the elucidation of a novel class of cytbc1 complex potent inhibitors with comparable binding energies and biological a...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 18, 2017 Category: Bioinformatics Source Type: research

Network Analysis of MPO and Other Relevant Proteins Involved in Diabetic Foot Ulcer and Other Diabetic Complications
In this study, we have used bioinformatics tools for the analysis of 24 genes that play a major role in diabetes mellitus and its complications, especially diabetic foot ulcer to reveal the relation between the genes and proteins involved in these disease conditions. We could conclude from the network model that MPO is related to foot ulcer and involved in pathogenesis of various co-associated diseases, such as oxidative stress, inflammation, peripheral vascular disease, and other related diabetes complications. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - September 13, 2017 Category: Bioinformatics Source Type: research

Structural Characterization of the Trimerization of TRAF6 Protein Through Molecular Dynamics Simulations
AbstractThe tumour necrosis factor (TNF) receptor-associated factor (TRAF) family of proteins having E3 ligase activity are the key molecules involved in cellular immune response pathways. TRAF6 is a unique member of the TRAF superfamily differing from other members of the family, owing to its specific interactions with molecules outside the TNF receptor superfamily. The C-terminal domain of TRAF proteins contains the catalytic residues and are known to be involved in self-oligomerization forming a mushroom-shaped trimeric structure, which is the functional form of the protein. However, the monomeric crystal structure of T...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 11, 2017 Category: Bioinformatics Source Type: research

Design of 2-Nitroimidazooxazine Derivatives as Deazaflavin-Dependent Nitroreductase (Ddn) Activators as Anti-Mycobacterial Agents Based on 3D QSAR, HQSAR, and Docking Study with In Silico Prediction of Activity and Toxicity
AbstractDeazaflavin-dependent nitroreductase (Ddn) is an emerging target in the field of anti-tuberculosis agents. In the present study, 2-nitroimidazooxazine derivatives as Ddn activators were aligned for CoMFA, CoMSIA and HQSAR analysis. The best CoMFA and CoMSIA model were generated with leave-one-out correlation coefficients (q2) of 0.585 and 0.571, respectively. Both the CoMFA and CoMSIA models were also validated by a test set of 11 compounds with satisfactory\(r^{ 2}_{\text{pred}}\) value of 0.701 and 0.667, respectively. Results of 3D QSAR and HQSAR study were used for the designing of novel and potent nitroimidazo...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 11, 2017 Category: Bioinformatics Source Type: research

In Silico Drug Design of Thiolactomycin Derivatives Against Mtb-KasA Enzyme to Inhibit Multidrug Resistance of Mycobacterium tuberculosis
AbstractTuberculosis (TB) is a leading infectious disease which kills a huge number of people every year over a decade, caused byMycobacterium tuberculosis. The conventional drugs in the market are no longer effective due to the increasing mycobacterial resistance to antibiotics. Hence, the need of finding efficient drugs to solve this multiple drug resistant factor is becoming an immediate issue. The first-line drugs in current practice for the treatment of TB emphasize on mycolic acid, which protects the bacteria from an immune response generated by the host. A key enzyme involved in this mycolic acid biosynthesis,M. tub...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 30, 2017 Category: Bioinformatics Source Type: research

Visualizing the Microscopic World
AbstractVisualization can be a motivating way of teaching students about the microscopic world. This can become even more exciting if the information is based on accurate computational results rather than on crude approximations that eventually might create unreal alternative perceptions. Here, we report on a VMD plug-in, named vmdMagazine, which can turn computational simulations into stunning high-impact video presentations, suitable for classes/lectures and even conferences. The software will help students/audience to understand atoms and molecules better and learn to like them. The present paper is meant to give a gene...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 9, 2017 Category: Bioinformatics Source Type: research

Reconstructing Genetic Regulatory Networks Using Two-Step Algorithms with the Differential Equation Models of Neural Networks
ConclusionThe unstable estimation of RNN using experimental time series having limited data points can lead to fairly arbitrary predicted GRNs. Our methods incorporate RNN and RMLP into a two-step structure learning procedure. Results show that the RERMLP using the RMLP with a suitable number of latent nodes to reduce the parameter dimension often result in more accurate edge ranks than the RERNN using the regularized RNN on short simulated time series. Combining by a weighted majority voting rule the networks derived by the RERMLP-RNN using different numbers of latent nodes in step one to infer the GRN, the method perform...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 26, 2017 Category: Bioinformatics Source Type: research

System Biology Approach to Identify Potential Receptor for Targeting Cancer and Biomolecular Interaction Studies of Indole[2,1-a]Isoquinoline Derivative as Anticancerous Drug Candidate Against it
AbstractCancer is a public health concern which is spreading throughout the world. Different approaches have been employed to combat this disease. System biology approach has been used to understand the molecular mechanisms of drugs targeting cancer cell ’s receptor which have opened-up a window to develop effective drugs for it. We have demonstrated biomolecular interaction studies using the rational drug design of indole[2,1-a]isoquinoline derivative as a potent inhibitor against identified cancerous protein PIK3CA —a catalytic sub-unit of PI3 K family protein—and compared its affinity with FDA approved...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 26, 2017 Category: Bioinformatics Source Type: research

Identification of Lead Molecules in Garcinia mangostana L. Against Pancreatic Cholesterol Esterase Activity: An In Silico Approach
AbstractHypercholesterolemia is one of the major risk factors for the development and progression of atherosclerosis. Hence, inhibitors of cholesterol absorption have been investigated for decades as a strategy to prevent and treat cardiovascular diseases associated with hypercholesterolemia. Cholesterol esterase (CEase) in pancreatic juice plays a vital role in the hydrolysis of dietary cholesterol esters to cholesterol and fatty acids. Since inhibition of CEase might lead to a reduction of cholesterol absorption, an attempt is made in this study to identify lead molecules ofGarcinia mangostana by the in silico approach. ...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 24, 2017 Category: Bioinformatics Source Type: research

Clustering and Candidate Motif Detection in Exosomal miRNAs by Application of Machine Learning Algorithms
ConclusionThe machine learning algorithms for aforementioned objectives were applied successfully. This work elaborated utility of machine learning algorithms and language platforms to achieve the tasks of clustering and candidate motif detection in exosomal miRNAs. With the information on mentioned objectives, deeper insight would be gained for analyses of newly discovered miRNAs in exosomes which are considered to be circulating biomarkers. In addition, the execution of machine learning algorithms on various language platforms gives more flexibility to users to try multiple iterations according to their requirements. Thi...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 22, 2017 Category: Bioinformatics Source Type: research

In Silico Analysis of nsSNPs of Carp TLR22 Gene Affecting its Binding Ability with Poly I:C
This study serves as a guide for in vivo evaluation of impact of mutation on immune response mediated by teleost TLR22 gene. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - June 28, 2017 Category: Bioinformatics Source Type: research

In Silico Identification of Novel microRNAs and Targets Using EST Analysis in Allium cepa L.
AbstractmicroRNAs (miRNAs) are a newly discovered class of non-coding small RNAs roughly 22 nucleotides long. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation, apoptosis and stress responses. The identification of miRNAs and their targets is an important need to understand their roles in the development and physiology of sweet onion (Allium cepa). In this research, several computational approaches were combined to make concise prediction of the potential miRNAs and their targets. We used previously known miRNAs from other plant species against ...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 28, 2017 Category: Bioinformatics Source Type: research

Studies of the Interaction of Influenza Virus RNA Polymerase PA N with Endonuclease Inhibitors
In this study, the docking and molecular dynamics simulations have been performed to explore the interaction of three kinds of endonuclease inhibitors with the subunit (PAN) of RNA polymerase. Our calculations indicate that all these endonuclease inhibitors can bind to the binding pocket of PAN, in which the electronegative oxygen atoms of the inhibitors form a chelated structure with the two Mn2+ cations of the active center. The most important interaction between these inhibitors and PAN is electrostatic interaction. The electron density of the chelate oxygen atoms determines the magnitude of the electrostatic energy, an...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 19, 2017 Category: Bioinformatics Source Type: research

In Silico Investigations of Chemical Constituents of Clerodendrum colebrookianum in the Anti-Hypertensive Drug Targets: ROCK, ACE, and PDE5
AbstractUnderstanding the molecular mode of action of natural product is a key step for developing drugs from them. In this regard, this study is aimed to understand the molecular-level interactions of chemical constituents ofClerodendrum colebrookianum Walp., with anti-hypertensive drug targets using computational approaches. The plant has ethno-medicinal importance for the treatment of hypertension and reported to show activity against anti-hypertensive drug targets —Rho-associated coiled-coil protein kinase (ROCK), angiotensin-converting enzyme, and phosphodiesterase 5 (PDE5). Docking studies showed that three che...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 16, 2017 Category: Bioinformatics Source Type: research

Identification of Strategic Residues at the Interface of Antigen –Antibody Interactions by In Silico Mutagenesis
AbstractStructural information pertaining to antigen –antibody interactions is fundamental in immunology, and benefits structure-based vaccine design. Modeling of antigen–antibody immune complexes from co-crystal structures or molecular docking simulations provides an extensive profile of the epitope at the interface; however, the key amino acids involved in the interaction must be further clarified, often through the use of experimental mutagenesis and subsequent binding assays. Here, we describe an in silico mutagenesis method to identify key sites at antigen–antibody interfaces, using significant incre...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 30, 2017 Category: Bioinformatics Source Type: research

In Silico Identification and Validation of Potential microRNAs in Kinnow Mandarin ( Citrus reticulata Blanco)
AbstractMicroRNAs (miRNAs) are a large family of 19 –25 nucleotides, regulatory, non-coding RNA molecules that control gene expression by cleaving or inhibiting the translation of target gene transcripts in animals and plants. Despite the important functions of miRNAs related to regulation of plant growth and development processes, metabolism, and abiotic and biotic stresses, little is known about the disease-related miRNA. Here, we present a new pipeline for miRNA analysis using expressed sequence tags (ESTs)-based bioinformatics approach in Kinnow mandarin, a commercially important citrus fruit crop. For this, 56,0...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 22, 2017 Category: Bioinformatics Source Type: research

Development of In Silico Protocols to Predict Structural Insights into the Metabolic Activation Pathways of Xenobiotics
AbstractTo establish in silico model to predict the structural insight into the metabolic bioactivation pathway of xenobiotics, we considered two specific and one non-specific mammary procarcinogen [e.g., dibenzo[a,l]pyrene (DBP), 7,12-dimethylbenz[a]anthracene (DMBA), and benzo[a]pyrene (BP)]. The CYP1A1, 1B1, 2C9, 1A2 and 2B6 reported in wet-lab studies to actively metabolize DBP also showed strong binding energies (kcal/mol) of −11.50, −10.67, −10.37, −9.76 and −9.72, respectively, with inhibition constants ranging between 0.01 and 0.08 µM. The CYP3A4 depicted minimum binding ene...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 19, 2017 Category: Bioinformatics Source Type: research

Quantitative prediction of drug side effects based on drug-related features
In conclusion, the proposed method is promising for the quantitative prediction of side effects, which may work cooperatively with existing state-of-the-art methods to reveal dangers of drugs. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - May 17, 2017 Category: Bioinformatics Source Type: research

Discovery of Therapeutic Lead Molecule Against β-Tubulin Using Computational Approach
AbstractVirtual screening strategy was performed against the target β-tubulin to overcome paclitaxel resistance in blood cancer types. In essence, A185T and A248V are two such important mutations frequently observed in clinical trials that confer paclitaxel resistance. In the present investigation, compounds from NPACT database were filtered by pharmacokinetics, to xicity and binding energy values. A total of 5 active compounds were identified from a list of 1574 bioactive compounds investigated in our study. Finally, we have compiled all the characteristic features into biologically meaningful clusters by hierarchica...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 9, 2017 Category: Bioinformatics Source Type: research

Inhibition of Gelatinases (MMP-2 and MMP-9) by Withania somnifera Phytochemicals Confers Neuroprotection in Stroke: An In Silico Analysis
AbstractA stroke or cerebrovascular accident is a serious, life-threatening medical condition that occurs when the blood supply to part of the brain is severely reduced or cut off, depriving brain tissue of oxygen and nutrients. Studies suggested that level of gelatinases (MMP-2 and MMP-9) usually increases in the brain after stroke. The elevated activity of gelatinases plays the deleterious role in ischemic stroke, hemorrhagic stroke and perinatal hypoxic –ischemic brain injury. Therefore, matrix metalloproteinase (MMP)-2 and MMP-9 inhibition have therapeutic importance in stroke condition. Present in silico study i...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 9, 2017 Category: Bioinformatics Source Type: research

Micelles, Rods, Liposomes, and Other Supramolecular Surfactant Aggregates: Computational Approaches
AbstractSurfactants are an interesting class of compounds characterized by the segregation of polar and apolar domains in the same molecule. This peculiarity makes possible a whole series of microscopic and macroscopic effects. Among their features, their ability to segregate particles (fluids or entire domains) and to reduce the surface/interfacial tension is the utmost important. The interest in the chemistry of surfactants never weakened; instead, waves of increasing interest have occurred every time a new field of application of these molecules has been discovered. All these special characteristics depend largely on th...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 6, 2017 Category: Bioinformatics Source Type: research

FPGASW: Accelerating Large-Scale Smith –Waterman Sequence Alignment Application with Backtracking on FPGA Linear Systolic Array
AbstractThe Smith –Waterman (SW) algorithm based on dynamic programming is a well-known classical method for high precision sequence matching and has become the gold standard to evaluate sequence alignment software. In this paper, we propose fine-grained parallelized SW algorithms using affine gap penalty and imple ment a parallel computing structures to accelerating the SW with backtracking on FPGA platform. We analysis the dynamic parallel computing features of anti-diagonal elements and storage expansion problem resulting from backtracking stage, and propose a series of optimization strategies to eliminate data de...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 21, 2017 Category: Bioinformatics Source Type: research