Asymptotic Expansion Method with Respect to Small Parameter for Ternary Diffusion Models
AbstractTernary diffusion models lead to strongly coupled systems of PDEs. We choose the smallest diffusion coefficient as a small parameter in a power series expansion whose components fulfill relatively simple equations. Although this series is divergent, one can use its finite sums to derive feasible numerical approximations, e.g. finite difference methods (FDMs). (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - April 12, 2017 Category: Bioinformatics Source Type: research

Computational Comparison and Visualization of Viruses in the Perspective of Clinical Information
AbstractThis paper addresses the visualization of complex information using multidimensional scaling (MDS). MDS is a technique adopted for processing data with multiple features scattered in high-dimensional spaces. For illustrating the proposed techniques, the case of viral diseases is considered. The study evaluates the characteristics of 21 viruses in the perspective of clinical information. Several new schemes are proposed for improving the visualization of the MDS charts. The results follow standard clinical practice, proving that the method represents a valuable tool to study a large number of viruses. (Source: Inter...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 8, 2017 Category: Bioinformatics Source Type: research

Metrical Consistency NMF for Predicting Gene –Phenotype Associations
AbstractDiscovering gene –phenotype associations is significant to understand the disease mechanisms. Nonnegative matrix factorization (NMF) has been widely used in computational biology for its good performance and interpretability. In this paper, we proposed a novel metrical consistency NMF (MCNMF) method for candidate gene prioritization. The MCNMF method assume that phenotype similarities, calculated from various independent ways, should be consistent in case that the associations between genes and phenotypes are completely known. Experiment results show that our method can recover the gene–phenotype associ...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 8, 2017 Category: Bioinformatics Source Type: research

Structural Insight into the Mechanism of Dibenzo[ a,l ]pyrene and Benzo[ a ]pyrene-Mediated Cell Proliferation Using Molecular Docking Simulations
AbstractIn the proposed work, we have explicated the mechanism of dibenzo[a,l]pyrene (DBP) and benzo[a]pyrene (BP) modulated cell proliferation by assessing the plausible binding with CASPASES, BAX, Bcl-2, MDM2, p53, p21, p16, CylinD1-CDK4 complex, CylinE1-CDK2 complex, H-Ras, K-Ras, BRCA1, and BRCA2 through exploiting the inherent potential of AutoDock Tools 4.0. In silico findings revealed that potent carcinogenic metabolites of DBP (e.g., ( −)-anti-DBPDE and (+)-syn-DBPDE) and BP (e.g., (+)-anti-BPDE) exhibited better binding interactions to Caspase-9 than Caspase-8 and Caspase-3. Feeble interactions of BAX and Bc...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 3, 2017 Category: Bioinformatics Source Type: research

Virtual Screening for Potential Inhibitors of CTX-M-15 Protein of Klebsiella pneumoniae
AbstractThe Gram-negative bacteriumKlebsiella pneumoniae, responsible for a wide variety of nosocomial infections in immuno-deficient patients, involves the respiratory, urinary and gastrointestinal tract infections and septicemia. Extended spectrum β-lactamases (ESBL) belong to β-lactamases capable of conferring antibiotic resistance in Gram-negative bacteria. CTX-M-15, a prevalent ESBL reported from Enterobacteriaceae includingK. pneumoniae, was selected as a potent anti-bacterial target. To identify the novel drug-like compounds, structure-based screening procedure was employed against downloaded drug-like com...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 3, 2017 Category: Bioinformatics Source Type: research

Computational Approaches and Related Tools to Identify MicroRNAs in a Species: A Bird ’s Eye View
AbstractMicroRNAs (miRNAs) are a family of non-coding RNAs that play a central role in fine-tuning gene expression regulation. Over the past decade, identification and annotation of miRNAs have become a major focus in epigenomics research. However, detection and characterization of miRNA are challenging due to its small size (~22 nucleotide-long) and susceptibility to degradation. The difficulties involved in experimental prediction and characterization of miRNA coding genes have led to the development of in silico-based approaches. Although several algorithms have been developed in recent years, a comprehensive assessment...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 30, 2017 Category: Bioinformatics Source Type: research

IR Spectra of Different O 2 -Content Hemoglobin from Computational Study: Promising Detector of Hemoglobin Variant in Medical Diagnosis
AbstractIR spectra of heme and different O2-content hemoglobin were studied by the quantum computation method at the molecule level. IR spectra of heme and different O2-content hemoglobin were quantificationally characterized from 0 to 100 THz. The IR spectra of oxy-heme and de-oxy-heme are obviously different at the frequency regions of 9.08 –9.48, 38.38–39.78, 50.46–50.82, and 89.04–91.00 THz. At 24.72 THz, there exists the absorption peak for oxy-heme, whereas there is not the absorption peak for de-oxy-heme. Whether the heme contains Fe–O–O bond or not has the great influence on its ...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 28, 2017 Category: Bioinformatics Source Type: research

EGFR gene regulation in colorectal cancer cells by garlic phytocompounds with special emphasis on S-Allyl-L-Cysteine Sulfoxide
AbstractColorectal cancer is one among the most common cancers in the world and a major cause of cancer related deaths. Similar to other cancers, colorectal carcinogenesis is often associated with over expression of genes related to cell growth and proliferation, especially Epidermal Growth Factor Receptor (EGFR). There is an increasing attention towards the plant derived compounds in prevention of colorectal carcinogenesis by downregulating EGFR. Among plants, garlic (Allium sativum L.) is emerging with anticancer properties by virtue of its organosulfur compounds. The present study was aimed to analyze the interaction ab...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 27, 2017 Category: Bioinformatics Source Type: research

Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers
AbstractLarge collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction. In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set. Three analyses are accomplished, each for gaining a deeper understanding of the processes underlying leukaemia types and subtypes. First, the main disease groups are tested for differential expression against the healthy control as in a standard case-control study. Here, the basic knowledge on molecular mechanisms is confi...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 16, 2017 Category: Bioinformatics Source Type: research

Construction of a Comprehensive Protein –Protein Interaction Map for Vitiligo Disease to Identify Key Regulatory Elements: A Systemic Approach
AbstractVitiligo is an idiopathic disorder characterized by depigmented patches on the skin due to progressive loss of melanocytes. Several genetic, immunological, and pathophysiological investigations have established vitiligo as a polygenetic disorder with multifactorial etiology. However, no definite model explaining the interplay between these causative factors has been established hitherto. Therefore, we studied the disorder at the system level to identify the key proteins involved by exploring their molecular connectivity in terms of topological parameters. The existing research data helped us in collating 215 protei...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 13, 2017 Category: Bioinformatics Source Type: research

Molecular Docking Studies to Explore Potential Binding Pockets and Inhibitors for Chikungunya Virus Envelope Glycoproteins
In this study, using two available crystal structures of the immature and mature forms of envelope glycoproteins, virtual screenings based on blind dockings and focused dockings were carried out to identify potential binding pockets and hit compounds for the virus. The chemical library database of compounds, NCI Diversity Set II, was used in these docking studies. In addition to reproducing previously reported examples, new binding pockets were identified, e.g., Pocket 2 in the 3N40, and Pocket 2 and Pocket 3 in the 3N42. Convergences in conformational sampling in docking using AutoDock Vina were evaluated. An analysis of ...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 11, 2017 Category: Bioinformatics Source Type: research

An Agent-Based Clustering Approach for Gene Selection in Gene Expression Microarray
AbstractGene selection is a major research area in microarray analysis, which seeks to discover differentially expressed genes for a particular target annotation. Such genes also often called informative genes are able to differentiate tissue samples belonging to different classes of the studied disease. Despite the fact that there is a wide number of proposals, the complexity imposed by this problem remains a challenge today. This research proposes a gene selection approach by means of a clustering-based multi-agent system. This proposal manages different filter methods and gene clustering through coordinated agents to di...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 9, 2017 Category: Bioinformatics Source Type: research

Structural Evaluation and Binding Mode Analysis of CCL19 and CCR7 Proteins —Identification of Novel Leads for Rheumatic and Autoimmune Diseases: An Insilico study
AbstractThe Human Chemokine (C –C motif) ligand 19 (CCL19) protein plays a major role in rheumatic and autoimmune diseases. The 3D models of the CCL19 and its receptor CCR7 are generated using homology modeling and are validated using standard computational protocols. Disulfide bridges identified in 3D model of CCL19 protein gi ve extra stability to the overall protein structure. The active site region of protein CCL19, containing N-terminal amino acid residues (Gly22 to Leu31), is predicted usingin silico techniques. Protein –protein docking studies are carried out between the CCL19 and CCR7 proteins to analys...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 7, 2017 Category: Bioinformatics Source Type: research

Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells
In this study, we will analyze four different algorithms (MBA, mCADRE, tI NIT and FASTCORE) for tissue-specific model reconstruction, based on a template model and two types of data sources: transcriptomics and proteomics. These methods will be applied to the reconstruction of metabolic models for hepatocyte cells and HepG2 cancer cell line. The models will be analyzed an d compared under different perspectives, emphasizing their functional analysis considering a set of metabolic liver tasks. The results show that there is no “ideal” algorithm. However, with the current analysis, we were able to retrieve knowle...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 2, 2017 Category: Bioinformatics Source Type: research

A New Decision Tree to Solve the Puzzle of Alzheimer ’s Disease Pathogenesis Through Standard Diagnosis Scoring System
AbstractAlzheimer ’s disease (AD) is a progressive, incurable and terminal neurodegenerative disorder of the brain and is associated with mutations in amyloid precursor protein, presenilin 1, presenilin 2 or apolipoprotein E, but its underlying mechanisms are still not fully understood. Healthcare sector is generat ing a large amount of information corresponding to diagnosis, disease identification and treatment of an individual. Mining knowledge and providing scientific decision-making for the diagnosis and treatment of disease from the clinical dataset are therefore increasingly becoming necessary. The curre nt stu...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 1, 2017 Category: Bioinformatics Source Type: research

An Algorithm for Sequencing by Hybridization Based on an Alternating DNA Chip
AbstractSequencing by hybridization allows the reconstruction of the DNA string of a given length from smaller fragments. These fragments are obtained in the hybridization experiment in which the DNA hybridizes to a DNA chip. In a classical approach, the chip consists of all oligonucleotides of a given length, with only one type of oligonucleotide for each probe of the chip. In this paper, we propose an algorithm solving the non-classical case of SBH, where the chip probes consist set of oligonucleotides described by some specific pattern. We will present the definition of such a non-classical DNA chip and the algorithm so...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 28, 2017 Category: Bioinformatics Source Type: research

Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods
AbstractGenome-scale metabolic models (GSMMs) have become important assets for rational design of compound overproduction using microbial cell factories. Most computational strain optimization methods (CSOM) using GSMMs, while useful in metabolic engineering, rely on the definition of questionable cell objectives, leading to some bias. Metabolic pathway analysis approaches do not require an objective function. Though their use brings immediate advantages, it has mostly been restricted to small scale models due to computational demands. Additionally, their complex parameterization and lack of intuitive tools pose an importa...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 25, 2017 Category: Bioinformatics Source Type: research

Novel Insight from Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium difficile
This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets ofClostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase. The three-dimensional structures...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 20, 2017 Category: Bioinformatics Source Type: research

Design, Synthesis, and Antibacterial Activities of Novel Heterocyclic Arylsulphonamide Derivatives
AbstractDesign, synthesis, and antibacterial activities of a series of arylsulphonamide derivatives as probable peptide deformylase (PDF) inhibitors have been discussed. Compounds have been designed following Lipinski ’s rule and after docking into the active site of PDF protein (PDB code: 1G2A) synthesized later on. Furthermore, to assess their antibacterial activity, screening of the compound was done in vitro conditions against Gram-positive and Gram-negative bacterial strains. In silico, studies revealed th ese compounds as potential antibacterial agents and this fact was also supported by their prominent scoring...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 13, 2017 Category: Bioinformatics Source Type: research

CAsubtype: An R Package to Identify Gene Sets Predictive of Cancer Subtypes and Clinical Outcomes
In conclusion, CAsubtype is a flexible and well-integrated tool in the R environment to identify gene sets for cancer subtype identification and clinical outcome prediction. Its simple R commands and comprehensive data sets enable efficient examination of the clinical value of any given gene set, thus facilitating hypothesis generating and testing in biological and clinical studies. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - January 21, 2017 Category: Bioinformatics Source Type: research

Change in Glutenin Macropolymer Secondary Structure in Wheat Sourdough Fermentation by FTIR
AbstractWheat sourdough was prepared by fermentation withLactobacillus plantarum M616 and yeast in the present study. The change in secondary structure of glutenin macropolymer (GMP) in wheat sourdough fermentation for 4 and 12  h was determined using Fourier transform infrared spectroscopy, and then the resultant spectra were Fourier self-deconvoluted of the amide I band in the region from 1600 to 1700 cm−1. Significant different spectra especially in the amide I band for GMP from sourdough fermented withL. plantarum M616 (SL) and withL. plantarum M616 and yeast (SLY) were found in respect of control dough...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 24, 2016 Category: Bioinformatics Source Type: research

Theoretical Studies on Azaindoles as Human Aurora B Kinase Inhibitors: Docking, Pharmacophore and ADMET Studies
AbstractAurora kinases are the cell cycle mitotic regulators processing multiple functions during cell division. Altered mechanism of these mitotic kinases may contribute to genomic instability that is most often correlated with tumorigenesis, which has been reported in manyhuman cancers. Selective blockage of the aberrantly expressed Aurora kinases has the potential therapeutic assessment to control the deregulated cell cycle machinery and their associated risks of cancer. Using a combination of docking-, ligand- and structure-based pharmacophore strategies, in the present study, we have tried to predict the anticancer po...
Source: Interdisciplinary Sciences, Computational Life Sciences - December 16, 2016 Category: Bioinformatics Source Type: research

Understanding the Interactions of High-Mobility Group of Protein Domain B1 with DNA Adducts Generated by Platinum Anticancer Molecules Using In Silico Approaches
AbstractPlatinum coordination compounds having cis geometry are frequently prescribed for various types of cancers. Protein dysregulation is one of the major factors contributing towards cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the cancers where platinum-based compounds are used either alone or in combination with radiation as therapy. The underlying interactions of these compounds with both DNA and proteins are crucial for the drug response. The compounds forms DNA adducts which are recognized by conserved, non-chromosomal high-mobility group box 1 (HMGB1) proteins. In the present study, ...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 30, 2016 Category: Bioinformatics Source Type: research

Significant Role of Segmental Duplications and SIDD Sites in Chromosomal Translocations of Hematological Malignancies: A Multi-parametric Bioinformatic Analysis
AbstractRecurrent non-random chromosomal translocations are hallmark characteristics of leukemogenesis, and however, molecular mechanisms underlying these rearrangements are less explored. The fundamental question is, why and how chromosomes break and reunite so precisely in the genome. Meticulous understanding of mechanism leading to chromosomal rearrangement can be achieved by characterizing breakpoints. To address this hypothesis, a novel multi-parametric computational approach for characterization of major leukemic translocations within and around breakpoint region was performed. To best of our knowledge, this bioinfor...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 28, 2016 Category: Bioinformatics Source Type: research

Molecular Interactions, Structural Transitions and Alterations in SoxB Protein Due to SoxYZ Interaction from Two Distinct β-Proteobacteria: An In silico Approach Towards the Thiosulfate Oxidation and Recycling of SoxY Protein
AbstractMicrobial oxidation –reduction reactions utilizing the environmental thiosulfate ions and mediated mainly by thesox operon are very much essential to maintain the sulfur balance in the environment. Majority of the previously documented wet laboratory studies show genetics behind the functionality of Sox proteins encoded by thesox operon. However, the molecular details of the involvements of the essential SoxB, SoxY and SoxZ proteins in the beta-proteobacteria have not yet been elucidated. In this work, an attempt was made to analyze the interaction profiles of the aforementioned SoxB, SoxY and SoxZ proteins t...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 28, 2016 Category: Bioinformatics Source Type: research

Portraying the Effect of Calcium-Binding Proteins on Cytosolic Calcium Concentration Distribution Fractionally in Nerve Cells
AbstractNerve cells like neurons and astrocytes in central nervous system (CNS) take part in the signaling process which means the transformation of the information from one cell to another via signals. The signaling process is affected by various external parameters like buffers calcium-binding proteins, voltage-gated calcium channel. In the present paper, the role of buffers in the cytoplasmic calcium concentration distribution is shown. The elicitation in calcium concentration is due to the presence of lower amount calcium-binding proteins which can be shown graphically. The mathematical model is designed by keeping in ...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 23, 2016 Category: Bioinformatics Source Type: research

Structural Insight into Binding Mode of 9-Hydroxy Aristolochic Acid, Diclofenac and Indomethacin to PLA 2
AbstractPhospholipase A2 (PLA2) catalyzes the hydrolysis of phospholipids into arachidonic acid and lysophospholipids. Arachidonic acid is modified by cyclooxygenases into active compounds called eicosanoids that act as signaling molecules in a number of physiological processes. Excessive production of eicosanoids leads to several pathological conditions such as inflammation. In order to block the inflammatory effect of these compounds, upstream enzymes such as PLA2 are valid targets. In the present contribution, molecular dynamic analysis was performed to evaluate the binding of diclofenac, 9-hydroxy aristolochic acid (9-...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 22, 2016 Category: Bioinformatics Source Type: research

An Improved Protein Surface Extraction Method Using Rotating Cylinder Probe
AbstractFor extraction of information on binding sites of a protein, the commonly known geometry-based methods utilize the corresponding PDB file to extract its surface as a first step. Finally, the surface is used to find the binding site atoms. As shown in this paper work, since none of the mostly used surface extraction methods can retrieve a sizeable percentage of the binding site atoms, the scope of development of a better method remains. In this direction, this paper presents a new benchmarking criteria based on utilization of binding site information to compare performance of these surface extraction methods. Also, ...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 22, 2016 Category: Bioinformatics Source Type: research

Exceptional Symmetry by Genomic Word
We present a detailed study of the exceptional symmetry by symmetric pairs and take the CG content into account. We also introduce and discuss the exceptional symmetry profile for the DNA of each organism, and we perform a multiple comparison for 31 genomes: 7 viruses; 5 archaea; 5 bacteria; 14 eukaryotes. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - November 19, 2016 Category: Bioinformatics Source Type: research

Comparing Performances of Multiple Comparison Methods in Commonly Used 2  ×  C Contingency Tables
This study aims at mentioning briefly multiple comparison methods such as Bonferroni, Holm –Bonferroni, Hochberg, Hommel, Marascuilo, Tukey, Benjamini–Hochberg and Gavrilov–Benjamini–Sarkar for contingency tables, through the data obtained from a medical research and examining their performances by simulation study which was constructed as the total 36 scenarios to 2 × 4 contin gency table. As results of simulation, it was observed that when the sample size is more than 100, the methods which can preserve the nominal alpha level are Gavrilov–Benjamini–Sarkar, Holm–B...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 16, 2016 Category: Bioinformatics Source Type: research

Targeting Heat Shock Proteins 60 and 70 of Toxoplasma gondii as a Potential Drug Target: In Silico Approach
AbstractHeat shock proteins (Hsps) 60 and 70 are postulated as a potential drug target for toxoplasmosis due to its importance in the developmental and survival ofToxoplasma gondii (T. gondii). As of today, there have been no reports on three-dimensional (3D) structure of Hsp60 and Hsp70 deposited in the Brookhaven Protein Data Bank. Hence, this study was conducted to predict 3D structures for Hsp60 and Hsp70 inT. gondii by homology modeling. Selection of the best predicted model was done based on multiple scoring functions. In addition, virtual screening was performed to short-list chemical compounds from the National Can...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 16, 2016 Category: Bioinformatics Source Type: research

Predicting the Binding Affinity of ER β Ligands Based on a Novel Variable Selection Method
AbstractA number of descriptors were employed to characterize the molecular structures of the 128 estrogen receptorβ ligands. A quantitative structure –activity relationship (QSAR) model of these compounds was developed by the variable selection method based on variable interaction. The QSAR model with five descriptors was internally and externally validated. The determination coefficient (R2) and the leave-one-out cross-validated correlation coefficient (Q2) are 0.8272 and 0.8041, respectively. The estimated correlation coefficient of the external validation is 0.8255. The mechanistic interpretation of the fina...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 16, 2016 Category: Bioinformatics Source Type: research

Computational Analysis and Binding Site Identification of Type III Secretion System ATPase from Pseudomonas aeruginosa
AbstractIn many gram-negative bacteria, the type III secretion system (T3SS), as a virulence factor, is an attractive target for developing novel antibacterial. Regarding this, in our study, we aimed to identify the putative drug target forPseudomonas aeruginosa, considering ATPase enzyme involved in the type III secretion system. Selective protein sequence ofP. aeruginosa involved in the T3SS was retrieved from NCBI databases, and its homologues were subjected to phylogenetic analysis. Its association in T3SS was analyzed via STRING, and the 3D structure was determined by means of homology modeling followed by intensive o...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 16, 2016 Category: Bioinformatics Source Type: research

Comparative Inhibition Study of Compounds Identified in the Methanolic Extract of Apamarga Kshara Against Trichomonas vaginalis Carbamate Kinase (TvCK): An Enzoinformatics Approach
Abstract In the present study, we have identified ten compounds, namely dodecanol acid, myristic acid, neophytadiene, palmitic acid, heptadecanoic acid, linoleic acid, elaidic acid, 3-7-dimethyl acid, stearic acid and methyl eicos acid, of the methanolic extract ofApamarga Kshara by GC –MS analysis.Apamarga Kshara has been reported to be active against cervical erosion. Major causal organism for cervical erosion isTrichomonas vaginalis. However, there is a paucity of information about the mechanism of action and inhibitory effect of the biologically active natural compounds presented inA. Kshara against this organi...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 16, 2016 Category: Bioinformatics Source Type: research

Microwave-Assisted ZrSiO 2 Catalysed Synthesis, Characterization and Computational Study of Novel Spiro[Indole-Thiazolidines] Derivatives as Anti-tubercular Agents
AbstractIn the current investigation, we prepared a series of novel spiro[indole-thiazolidines] derivatives (5a–5h) from 5-substituted isatin derivatives and thioglycolic acid (TGA) with ZrSiO2 as an efficient catalyst under microwave irradiation. The significant merits of this protocol have some significant merits such as simplicity in operation, simple, efficient workup, good practical yields of product and the employment of recyclable catalyst. All the new synthesized scaffold has been well characterized by various spectroscopic methods and elemental analysis. All the spiro scaffolds were subjected to in vitro ant...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 11, 2016 Category: Bioinformatics Source Type: research

Rectified-Linear-Unit-Based Deep Learning for Biomedical Multi-label Data
AbstractDisease diagnosis is one of the major data mining questions by the clinicians. The current diagnosis models usually have a strong assumption that one patient has only one disease,i.e. a single-label data mining problem. But the patients, especially when at the late stages, may have more than one disease and require a multi-label diagnosis. The multi-label data mining is much more difficult than a single-label one, and very few algorithms have been developed for this situation. Deep learning is a data mining algorithm with highly dense inner structure and has achieved many successful applications in the other areas....
Source: Interdisciplinary Sciences, Computational Life Sciences - November 11, 2016 Category: Bioinformatics Source Type: research

A Computational Systems Biology Approach for Identifying Candidate Drugs for Repositioning for Cardiovascular Disease
We report an in silico method to screen for receptors or pathways that could be targeted to elicit beneficial transcriptional changes in a cellular model of a disease of interest. In our method, we integrate: (1) a dataset of transcriptome responses of a cell line to a panel of drugs; (2) two sets of genes for the disease; and (3) mappings between drugs and the receptors or pathways that they target. We carried out a gene set enrichment analysis (GSEA) test for each of the two gene sets against a list of genes ordered by fold-change in response to a drug in a relevant cell line (HL60), with the overall score for a drug bei...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 24, 2016 Category: Bioinformatics Source Type: research

A New SEYHAN ’s Approach in Case of Heterogeneity of Regression Slopes in ANCOVA
In this study, when the assumptions of linearity and homogeneity of regression slopes of conventional ANCOVA are not met, a new approach named asSEYHAN has been suggested to use conventional ANCOVA instead of robust or nonlinear ANCOVA. The proposedSEYHAN ’s approach involves transformation of continuous covariate into categorical structure when the relationship between covariate and dependent variable is nonlinear and the regression slopes are not homogenous. A simulated data set was used to explainSEYHAN ’s approach. In this approach, we performed conventional ANCOVA in each subgroup which is constituted acco...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 18, 2016 Category: Bioinformatics Source Type: research

Predicting the Organelle Location of Noncoding RNAs Using Pseudo Nucleotide Compositions
Abstract Noncoding RNAs (ncRNAs) are implicated in various biological processes. Recent findings have demonstrated that the function of ncRNAs correlates with their provenance. Therefore, the recognition of ncRNAs from different organelle genomes will be helpful to understand their molecular functions. However, the weakness of experimental techniques limits the progress toward studying organellar ncRNAs and their functional relevance. As a complement of experiments, computational method provides an important choice to identify ncRNA in different organelles. Thus, a computational model was developed to identify ncRNAs fro...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 13, 2016 Category: Bioinformatics Source Type: research

Improving Allergen Prediction in Main Crops Using a Weighted Integrative Method
AbstractAs a public health problem, food allergy is frequently caused by food allergy proteins, which trigger a type-I hypersensitivity reaction in the immune system of atopic individuals. The food allergens in our daily lives are mainly from crops including rice, wheat, soybean and maize. However, allergens in these main crops are far from fully uncovered. Although some bioinformatics tools or methods predicting the potential allergenicity of proteins have been proposed, each method has their limitation. In this paper, we built a novel algorithm PREALW, which integrated PREAL, FAO/WHO criteria and motif-based method by a ...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 12, 2016 Category: Bioinformatics Source Type: research

The Topology Prediction of Membrane Proteins: A Web-Based Tutorial
This study presents an alternative education material to the students in biochemistry laboratories in addition to classical laboratory experiments. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - October 7, 2016 Category: Bioinformatics Source Type: research

Evaluation and Elucidation Studies of Natural Aglycones for Anticancer Potential using Apoptosis-Related Markers: An In silico Study
AbstractExposure to exogenous and endogenous chemicals and subsequent cellular and molecular changes has been linked to enhanced cell proliferation and restricted apoptosis phenomenon. Though in the past decades numerous anticancer drugs inducing programmed cell death in cancer cells by targeting specific apoptotic markers have reached the market, they have been allied with unwanted side effects, ranging from mild to severe toxicity. With further understanding on the functional mechanism of p53 and MDM2 in apoptosis and in our continuous search for new and potent multi-target anticancer lead compounds, we have carried out ...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 5, 2016 Category: Bioinformatics Source Type: research

Structure-Based Drug Designing and Simulation Studies for Finding Novel Inhibitors of Heat Shock Protein (HSP70) as Suppressors for Psoriasis
AbstractPsoriasis is a chronic immune-mediated inflammatory skin disorder. Heat shock proteins (HSPs) have been witnessed as a potential drug target for inhibition of psoriatic cell differentiation. The expression level of HSP is increased when the cells get exposed to elevated temperature, oxidative stress and nutritional deficiencies and thus plays major role in psoriatic progression pathway. Immunoreactivity intensity distribution index scores for HSP70 expression is significantly higher in psoriatic patients compared to normal. In the present work, the 3D structure of human Hsp70 has been taken. Inhibition of HSP70 can...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 1, 2016 Category: Bioinformatics Source Type: research

Bioactivity of Marine Streptomyces sp. VITJS4: Interactions of Cytotoxic Phthalate Derivatives with Human Topoisomerase II α: An In Silico Molecular Docking Analysis
AbstractDespite clinical advances in antimicrobial and anticancer therapy, there is an urge for the search of new bioactive compounds. In the present study, previously isolatedStreptomyces sp. VITJS4 strain (NCIM No. 5574) (ACC No: JQ234978.1) crude extract tested for antibacterial activity showed a broad spectrum at the concentration of 20  mg/mL against pathogens. The antioxidant potential tested at 0.5 mg/mL concentration exhibited reducing power activity with a maximum of 90 % inhibition. The anticancer property by MTT assay on HeLa and HepG2 cells showed cytotoxic effect with IC50 of 50  µg/m...
Source: Interdisciplinary Sciences, Computational Life Sciences - October 1, 2016 Category: Bioinformatics Source Type: research

Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations
This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - October 1, 2016 Category: Bioinformatics Source Type: research

LPRP: A Gene –Gene Interaction Network Construction Algorithm and Its Application in Breast Cancer Data Analysis
In this study, we propose a novel GGI network construction method called linear and probabilistic relations prediction (LPRP) and used it for gaining system level insight into breast cancer mechanis ms. We construct separate genome-wide GGI networks for tumor and normal breast samples, respectively, by applying LPRP on their gene expression datasets profiled by The Cancer Genome Atlas. According to our analysis, a large loss of gene interactions in the tumor GGI network was observed (7436; 88.7  % reduction), which also contained fewer functional genes (4757; 32 % reduction) than the normal network. Tumor GGI net...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 17, 2016 Category: Bioinformatics Source Type: research

Designing of Epitope-Focused Vaccine by Targeting E6 and E7 Conserved Protein Sequences: An Immuno-Informatics Approach in Human Papillomavirus 58 Isolates
AbstractHuman papillomavirus (HPV) is a DNA virus that belongs to the papillomavirus family and is capable of infecting humans. Currently, few vaccines are available to prevent infection by HPV. However, they are not so much effective and provide little benefit to women who have already been infected with HPV. The aim of this study was to design epitope-based vaccines of HPV58 by targeting E6 and E7 proteins of HPV58. Proteomic sequences were retrieved from different isolates at different time periods and later analyzed by performing alignment of these sequences. To ensure the capacity of humoral and cell-mediated immunity...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 17, 2016 Category: Bioinformatics Source Type: research

A Novel Hybrid Feature Selection Model for Classification of Neuromuscular Dystrophies Using Bhattacharyya Coefficient, Genetic Algorithm and Radial Basis Function  Based Support Vector Machine
AbstractAn accurate classification of neuromuscular disorders is important in providing proper treatment facilities to the patients. Recently, the microarray technology is employed to monitor the level of activity or expression of large number of genes simultaneously. The gene expression data derived from the microarray experiment usually involve a large number of genes but a very few number of samples. There is a need to reduce the dimension of gene expression data which intends to find a small set of discriminative genes that accurately classifies the samples of various kinds of diseases. So, our goal is to find a small ...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 17, 2016 Category: Bioinformatics Source Type: research

Ganoderic Acid A Targeting β-Catenin in Wnt Signaling Pathway: In Silico and In Vitro Study
AbstractWnt signaling pathways are the group of signaling transduction controlling the embryonic development, cell proliferation, cell migration, cell fate specification, and body axis pattern. Nuclear accumulation of β-catenin in Wnt signaling is a widely recognized marker of poor cancer prognosis which regulates fat and glucose metabolism. Ganoderic acid is a triterpene isolated from fungusGanoderma lucidum renowned for its pharmacological effects. The present study revealed the mechanistic study of β-catenin with 50 isoforms of ganoderic acid by molecular docking using Maestro 9.6 (Schrödinger Inc) in Wnt...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 22, 2016 Category: Bioinformatics Source Type: research

Identification of Dual Natural Inhibitors for Chronic Myeloid Leukemia by Virtual Screening, Molecular Dynamics Simulation and ADMET Analysis
AbstractChronic myeloid leukemia (CML) is a disease of bone marrow stem cells caused by excessive growth and accumulation of granulocytes in the blood. Aberrant expression of the BCR-ABL proteins in bone marrow stem cells have found out in 95  % cases of CML. Tyrosine Kinase domains (SH2 and SH3) of BCR-ABL proteins are the potent targets to inhibit the process. Initially, imatinib is preferred as an efficient inhibitor to control functional activity of disease. Recently, it has been reported that the advanced stage of CML developed res istance against imatinib. In continuation, dasatinib is the first drug to combat a...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research