Functional Annotation and Analysis of Dual Oxidase 1 (DUOX1): a Potential Anti-pyocyanin Immune Component
In this study, we structurally and functionally annotated the DUOX1, predicted its 3d structure, physio-chemical properties, post-translational modifications, and genetic polymorphism analysis with subsequent disease-associated single-nucleotide variations and their impact on DUOX1 functionality by employing in silico approaches. DUOX1 holds greater homology with gorilla and chimpanzee than other primates. The localization signal peptide was present at the beginning of the peptide with cleavage site at 22 aa position. Three distinct functional domains were observed based on homology: An_peroxidase, FRQ1, and oxido-reductas...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 27, 2018 Category: Bioinformatics Source Type: research

Study of Molecular Mechanism of the Interaction Between MEK1/2 and Trametinib with Docking and Molecular Dynamic Simulation
In this study, the focus of investigation was the mechanism of the interaction between trametinib and MEK1/2 via computational simulation. To specify the best interaction site of inhibitor with MEK1/2 based on the interaction energy ranking, first we performed a docking and then we studied the interactions of the  ATP-bound MEK with trametinib, with RAF and the complex of the ATP-bound MEK–trametinib with RAF via molecular dynamic simulations. The results showed that trametinib inactivates the enzyme by bonding to a group of amino acids including Lys97/101, SER218/216, Asp208/212, and Met143/147 in MEK1/ 2....
Source: Interdisciplinary Sciences, Computational Life Sciences - November 21, 2018 Category: Bioinformatics Source Type: research

Ensemble Technique for Prediction of T-cell Mycobacterium tuberculosis Epitopes
AbstractDevelopment of an effective machine-learning model for T-cellMycobacterium tuberculosis (M. tuberculosis) epitopes is beneficial for saving biologist ’s time and effort for identifying epitope in a targeted antigen. Existing NetMHC 2.2, NetMHC 2.3, NetMHC 3.0 and NetMHC 4.0 estimate binding capacity of peptide. This is still a challenge for those servers to predict whether a given peptide isM. tuberculosis epitope or non-epitope. One of the servers, CTLpred, works in this category but it is limited to peptide length of 9-mers. Therefore, in this work direct method of predicting M. tuberculosis epitope or non-...
Source: Interdisciplinary Sciences, Computational Life Sciences - November 7, 2018 Category: Bioinformatics Source Type: research

An In-Silico Investigation of Key Lysine Residues and Their Selection for Clearing off A β and Holo-AβPP Through Ubiquitination
AbstractMalicious progression of neurodegeneration is a consequence of toxic aggregates of proteins or peptides such as amyloid beta (A β) reported in Alzheimer’s disease (AD). These aggregates hinder the electrochemical transmission at neuronal junctions and thus deteriorate neuronal-health by triggering dementia. Electrostatic and hydrophobic interactions among amino-acid residues are the governing principle behind the self-ass embly of aforesaid noxious oligomers or agglomerate. Interestingly, lysine residues are crucial for these interactions and for facilitating the clearance of toxic metabolites through th...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 7, 2018 Category: Bioinformatics Source Type: research

Computational Study of HCV p7 Channel: Insight into a New Strategy for HCV Inhibitor Design
AbstractHCV p7 protein is a cation-selective ion channel, playing an essential role during the life cycle of HCV viruses. To understand the cation-selective mechanism, we constructed a hexameric model in lipid bilayers of HCV p7 protein for HCB JFH-1 strain, genotype 2a. In this structural model, His9 and Val6 were key factors for the HCV cation-selective ion channel. The histidine residues at position 9 in the hexameric model formed a first gate for HCV p7 channel, acting as a selectivity filter for cations. The valines mentioned above formed a second gate for HCV p7 channel, serving as a hydrophobic filter for the dehydr...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 7, 2018 Category: Bioinformatics Source Type: research

An In-Silico Investigation of Key Lysine Residues and Their Selection for Clearing off A β and Holo-AβPP Through Ubiquitination
AbstractMalicious progression of neurodegeneration is a consequence of toxic aggregates of proteins or peptides such as amyloid beta (A β) reported in Alzheimer’s disease (AD). These aggregates hinder the electrochemical transmission at neuronal junctions and thus deteriorate neuronal-health by triggering dementia. Electrostatic and hydrophobic interactions among amino-acid residues are the governing principle behind the self-ass embly of aforesaid noxious oligomers or agglomerate. Interestingly, lysine residues are crucial for these interactions and for facilitating the clearance of toxic metabolites through th...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 7, 2018 Category: Bioinformatics Source Type: research

Computational Study of HCV p7 Channel: Insight into a New Strategy for HCV Inhibitor Design
AbstractHCV p7 protein is a cation-selective ion channel, playing an essential role during the life cycle of HCV viruses. To understand the cation-selective mechanism, we constructed a hexameric model in lipid bilayers of HCV p7 protein for HCB JFH-1 strain, genotype 2a. In this structural model, His9 and Val6 were key factors for the HCV cation-selective ion channel. The histidine residues at position 9 in the hexameric model formed a first gate for HCV p7 channel, acting as a selectivity filter for cations. The valines mentioned above formed a second gate for HCV p7 channel, serving as a hydrophobic filter for the dehydr...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 7, 2018 Category: Bioinformatics Source Type: research

Identification of Effective Dimeric Gramicidin-D Peptide as Antimicrobial Therapeutics over Drug Resistance: In-Silico Approach
In conclusion, g-AB peptide has definitely demonstrated adequate structural stability and functionality and this work will need to be considered in peptide-based drug discovery. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - September 4, 2018 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 - September 1, 2018 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 - September 1, 2018 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 - September 1, 2018 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 - September 1, 2018 Category: Bioinformatics Source Type: research

GC $$^2$$ 2 NMF: A Novel Matrix Factorization Framework for Gene –Phenotype Association Prediction
AbstractGene –phenotype association prediction can be applied to reveal the inherited basis of human diseases and facilitate drug development. Gene–phenotype associations are related to complex biological processes and influenced by various factors, such as relationship between phenotypes and that among gene s. While due to sparseness of curated gene–phenotype associations and lack of integrated analysis of the joint effect of multiple factors, existing applications are limited to prediction accuracy and potential gene–phenotype association detection. In this paper, we propose a novel method by expl...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 1, 2018 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 - September 1, 2018 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 - September 1, 2018 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 - September 1, 2018 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 - September 1, 2018 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 - September 1, 2018 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 - September 1, 2018 Category: Bioinformatics Source Type: research

IIKmTA: Inter and Intra Kingdom miRNA-Target Analyzer
ConclusionsRecent researches identified miRNAs in plants and human secretions and their role in regulating the human genes. Such findings indicate the therapeutic role of secretory miRNAs of such plants which exhibits medicinal value and in near future many diseases may be treated by consumption of these plant miRNAs through food. Using our newly developed database and analyzing tool, one can easily determine the different relationships between miRNAs and their targets across kingdoms. IIKmTA is freely available athttp://www.bioinformatics.org/iikmta/. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - September 1, 2018 Category: Bioinformatics Source Type: research

Genome-Wide Pathway Analysis of Microarray Data Identifies Risk Pathways Related to Salt Stress in Arabidopsis Thaliana
AbstractSalt stress is a common abiotic stress in agricultural production, which is affected by multiple genes and environmental factors. Although transcriptome analyses have detected some salt-related genes inArabidopsis thaliana, these genes are often major genes and can  not adequately explain the molecular mechanism of salt tolerance. Some genes related to salt stress, but does not reach significant threshold in gene expression analysis (called modest effect genes), are often ignored. Therefore, we took full account of the role of modest effect genes and performe d a pathway-based analysis of three gene microarray...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 1, 2018 Category: Bioinformatics Source Type: research

Study on Feature Selection Methods for Depression Detection Using Three-Electrode EEG Data
AbstractThe early diagnosis of depression is important to the treatment of this condition, whereas a timely diagnosis can reduce the incidence of mortality caused in patients with depression. In the present study, we collected the EEG signals of Fp2, Fpz and Fp1, compared with 128 channels EEG, a simpler test (3 channels EEG) can make diagnosis more accessible and widespread, researchers can perform more tests on more patients given the same amount of time and money. The difference between the depressed and the non-depressed patients was explored by the linear and non-linear characteristics of these EEG signals. A total of...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 1, 2018 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 - September 1, 2018 Category: Bioinformatics Source Type: research

An Efficient Design for a Multi-objective Evolutionary Algorithm to Generate DNA Libraries Suitable for Computation
AbstractThe design of reliable DNA libraries that can be used for bio-molecular computing involves several heterogeneous conflicting design criteria that traditional optimization approaches do not fit properly. As it is well known, evolutionary algorithms are very appropriate for solving complex NP-hard optimization problems. However, these approaches take significant computational resources when large instances of complex problems are managed. This is the case for the design of DNA libraries suitable for computation, which involves a set of conflicting design criteria that have to be simultaneously optimized. The problem ...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 30, 2018 Category: Bioinformatics Source Type: research

Structure-Based Virtual Screening of High-Affinity ATP-Competitive Inhibitors Against Human Lemur Tyrosine Kinase-3 (LMTK3) Domain: A Novel Therapeutic Target for Breast Cancer
AbstractHuman lemur tyrosine kinase-3 (LMTK3) is an oncogenic kinase known to regulate ER- α through phosphorylation and is considered to be a novel therapeutic target for breast cancer. In this work, we have studied the ATP-binding mechanism with LMTK3 domain and also carried out virtual screening on LMTK3 to identify lead compounds using Dock blaster server. The top scored compounds ob tained from Dock blaster were then narrowed down further to six lead compounds (ZINC37996511, ZINC83363046, ZINC3745998, ZINC50456700, ZINC83351792 and ZINC83364581) based on high-binding affinity and non-bonding interactions with LM...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 31, 2018 Category: Bioinformatics Source Type: research

GC $$^2$$ 2 NMF: A Novel Matrix Factorization Framework for Gene –Phenotype Association Prediction
AbstractGene –phenotype association prediction can be applied to reveal the inherited basis of human diseases and facilitate drug development. Gene–phenotype associations are related to complex biological processes and influenced by various factors, such as relationship between phenotypes and that among gene s. While due to sparseness of curated gene–phenotype associations and lack of integrated analysis of the joint effect of multiple factors, existing applications are limited to prediction accuracy and potential gene–phenotype association detection. In this paper, we propose a novel method by expl...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 24, 2018 Category: Bioinformatics Source Type: research

Transcription Factors Contribute to Differential Expression in Cellular Pathways in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma
AbstractLung cancers are broadly classified into small cell lung cancers and non-small cell lung cancers (NSCLC). Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are two common subtypes of NSCLC, and despite the fact that both occur in lung tissues, these two subtypes show a number of different pathological characteristics. To investigate the differences and seek potential therapy targets, we used bioinformatics methods to analyze RNA-Seq data from different aspects. The previous studies and comparative pathway enrichment analysis on publicly available data showed that expressed or inhibited genes are di...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 23, 2018 Category: Bioinformatics Source Type: research

Comparative Analysis of CRISPR Loci Found in Streptomyces Genome Sequences
In this study, we present the comparative analysis of 182 CRISPR loci found in 46 publicly available complete genome sequences ofStreptomyces. Overall, nine direct repeats (DRs) groups are identified while all the 2104 spacers are divided into three main groups according to the multiple sequence alignment. Only 11 spacers are identical with parts of 10 plasmid sequences, which indicates a possible origin. Thecas gene clusters near the CRISPR arrays are found to mainly belong to the I –E subtype. These CRISPR loci might play an important role in the genome evolution ofStreptomyces. (Source: Interdisciplinary Sciences,...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 20, 2018 Category: Bioinformatics Source Type: research

A Fast Projection-Based Algorithm for Clustering Big Data
AbstractWith the fast development of various techniques, more and more data have been accumulated with the unique properties of large size (tall) and high dimension (wide). The era of big data is coming. How to understand and discover new knowledge from these data has attracted more and more scholars ’ attention and has become the most important task in data mining. As one of the most important techniques in data mining, clustering analysis, a kind of unsupervised learning, could group a set data into objectives(clusters) that are meaningful, useful, or both. Thus, the technique has played ver y important role in kno...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 7, 2018 Category: Bioinformatics Source Type: research

Study on Feature Selection Methods for Depression Detection Using Three-Electrode EEG Data
AbstractThe early diagnosis of depression is important to the treatment of this condition, whereas a timely diagnosis can reduce the incidence of mortality caused in patients with depression. In the present study, we collected the EEG signals of Fp2, Fpz and Fp1, compared with 128 channels EEG, a simpler test (3 channels EEG) can make diagnosis more accessible and widespread, researchers can perform more tests on more patients given the same amount of time and money. The difference between the depressed and the non-depressed patients was explored by the linear and non-linear characteristics of these EEG signals. A total of...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 4, 2018 Category: Bioinformatics Source Type: research

Subtractive Genomics, Molecular Docking and Molecular Dynamics Simulation Revealed LpxC as a Potential Drug Target Against Multi-Drug Resistant Klebsiella pneumoniae
AbstractThe emergence and dissemination of pan drug resistant clones ofKlebsiella pneumoniae are great threat to public health. In this regard new therapeutic targets must be highlighted to pave the path for novel drug discovery and development. Subtractive proteomic pipeline brought forth UDP-3-O-[3-hydroxymyristoyl]N-acetylglucosamine deacetylase (LpxC), a Zn+2 dependent cytoplasmic metalloprotein and catalyze the rate limiting deacetylation step of lipid A biosynthesis pathway. Primary sequence analysis followed by 3-dimensional (3-D) structure elucidation of the protein led to the detection ofK. pneumoniae LpxC (KpLpxC...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 2, 2018 Category: Bioinformatics Source Type: research

GC $$^2$$ 2 NMF: A Novel Matrix Factorization Framework for Gene –Phenotype Association Prediction
AbstractGene –phenotype association prediction can be applied to reveal the inherited basis of human diseases and facilitate drug development. Gene–phenotype associations are related to complex biological processes and influenced by various factors, such as relationship between phenotypes and that among gene s. While due to sparseness of curated gene–phenotype associations and lack of integrated analysis of the joint effect of multiple factors, existing applications are limited to prediction accuracy and potential gene–phenotype association detection. In this paper, we propose a novel method by expl...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 24, 2018 Category: Bioinformatics Source Type: research

Construction of Transcriptional Regulatory Network of Alzheimer ’s Disease Based on PANDA Algorithm
AbstractThe focus of modern biomedical research concentrates on molecular level regulatory mechanisms and how the normal and abnormal phenotypes of tissue functional are affected by regulatory mechanisms. Most of the research on regulatory mechanism starts from the reconstruction of gene regulation network. At present, a large number of reconstruction methods construct the network using a single data set. These methods of inferring and predicting the relationship between the target gene and the transcription factor (TF) can be used to identify individual interactions between genes, while there is not much research on the i...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 19, 2018 Category: Bioinformatics Source Type: research

Review of CRISPR/Cas9 sgRNA Design Tools
AbstractThe adaptive immunity system in bacteria and archaea, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associate (CRISPR/Cas), has been adapted as a powerful gene editing tool and got a broad application in genome research field due to its ease of use and cost-effectiveness. The performance of CRISPR/Cas relies on well-designed single-guide RNA (sgRNA), so a lot of bioinformatic tools have been developed to assist the design of highly active and specific sgRNA. These tools vary in design specifications, parameters, genomes and so on. To help researchers to choose their proper tools, we reviewed var...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 11, 2018 Category: Bioinformatics Source Type: research

Modified Global Flower Pollination Algorithm and its Application for Optimization Problems
AbstractFlower Pollination Algorithm (FPA) has increasingly attracted researchers ’ attention in the computational intelligence field. This is due to its simplicity and efficiency in searching for global optimality of many optimization problems. However, there is a possibility to enhance its search performance further. This paper aspires to develop a new FPA variant that aims t o improve the convergence rate and solution quality, which will be called modified global FPA (mgFPA). The mgFPA is designed to better utilize features of existing solutions through extracting its characteristics, and direct the exploration pr...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 28, 2018 Category: Bioinformatics Source Type: research

Quantum Calculations on Plant Cell Wall Component Interactions
AbstractDensity functional theory calculations were performed to assess the relative interaction energies of plant cell wall components: cellulose, xylan, lignin and pectin. Monomeric and tetramer linear molecules were allowed to interact in four different configurations for each pair of compounds. The M05-2X exchange-correlation functional which implicitly accounts for short- and mid-range dispersion was compared against MP2 and RI-MP2 to assess the reliability of the former for modeling van der Waals forces between these PCW components. Solvation effects were examined by modeling the interactions in the gas phase, in exp...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 26, 2018 Category: Bioinformatics Source Type: research

IIKmTA: Inter and Intra Kingdom miRNA-Target Analyzer
ConclusionsRecent researches identified miRNAs in plants and human secretions and their role in regulating the human genes. Such findings indicate the therapeutic role of secretory miRNAs of such plants which exhibits medicinal value and in near future many diseases may be treated by consumption of these plant miRNAs through food. Using our newly developed database and analyzing tool, one can easily determine the different relationships between miRNAs and their targets across kingdoms. IIKmTA is freely available athttp://www.bioinformatics.org/iikmta/. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - March 16, 2018 Category: Bioinformatics Source Type: research

NeuroPP: A Tool for the Prediction of Neuropeptide Precursors Based on Optimal Sequence Composition
AbstractNeuropeptides (NPs) are short secreted peptides produced mainly in the nervous system and digestive system. They activate signaling cascades to control a wide range of biological functions, such as metabolism, sensation, and behavior. NPs are typically produced from a larger NP precursor (NPP) which includes a signal peptide sequence, one or more NP sequences, and other sequences. With the drastic growth of unknown protein sequences generated in the post-genomic age, it is highly desired to develop computational methods for identifying NPP rapidly and efficiently. In this article, we developed a predictor for NPPs ...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 10, 2018 Category: Bioinformatics Source Type: research

Computational Analysis of High-Risk SNPs in Human DBY Gene Responsible for Male Infertility: A Functional and Structural Impact
ConclusionTo the best of our knowledge, this is the first study to detect pathologically significant nsSNPs (G300D) through a computational approach in the DBY which can be useful for development in potent drug discovery studies. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - March 8, 2018 Category: Bioinformatics Source Type: research

Study on the Mechanisms of Active Compounds in Traditional Chinese Medicine for the Treatment of Influenza Virus by Virtual Screening
In this study, we focused on six influenza virus proteins that could be anti-influenza drug targets, including neuraminidase (NA), hemagglutinin (HA), matrix protein 1 (M1), M2 proton channel (M2), nucleoprotein (NP) and non-structural protein 1 (NS1). Structure-based molecular docking was utilized to identify potential inhibitors for these drug targets from 13144 compounds in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. The results showed that 56 compounds could inhibit more than two drug targets simultaneously. Further, we utilized reverse docking to study the interaction of these...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 2, 2018 Category: Bioinformatics Source Type: research

Genome-Wide Pathway Analysis of Microarray Data Identifies Risk Pathways Related to Salt Stress in Arabidopsis Thaliana
AbstractSalt stress is a common abiotic stress in agricultural production, which is affected by multiple genes and environmental factors. Although transcriptome analyses have detected some salt-related genes inArabidopsis thaliana, these genes are often major genes and can  not adequately explain the molecular mechanism of salt tolerance. Some genes related to salt stress, but does not reach significant threshold in gene expression analysis (called modest effect genes), are often ignored. Therefore, we took full account of the role of modest effect genes and performe d a pathway-based analysis of three gene microarray...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 28, 2018 Category: Bioinformatics Source Type: research

Systematic Analysis of Primary Sequence Domain Segments for the Discrimination Between Class C GPCR Subtypes
AbstractG-protein-coupled receptors (GPCRs) are a large and diverse super-family of eukaryotic cell membrane proteins that play an important physiological role as transmitters of extracellular signal. In this paper, we investigate Class C, a member of this super-family that has attracted much attention in pharmacology. The limited knowledge about the complete 3D crystal structure of Class C receptors makes necessary the use of their primary amino acid sequences for analytical purposes. Here, we provide a systematic analysis of distinct receptor sequence segments with regard to their ability to differentiate between seve...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 19, 2018 Category: Bioinformatics Source Type: research

MYOD and HAND transcription factors have conserved recognition sites in mTOR promoter: insights from in silico analysis
AbstractmTOR regulates multiple cellular processes that are critical for proper maintenance of cell growth and development. However, mechanisms and factors responsible for transcriptional regulation of mTOR are partially known. To identify different transcription factor binding sites in promoter region of mTOR, we performed in silico phylogenetic foot printing analysis of diverse set of human orthologs. Phylogenetic tree for the orthologs was generated to establish the evolutionary relationships among them. Conserved binding sites among the species were predicted by tool MEME. The predicted conserved sites were further ana...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 6, 2018 Category: Bioinformatics Source Type: research

Region-Specific Methylation Profiling in Acute Myeloid Leukemia
AbstractAlteration of DNA methylation level in cancer diseases leads to deregulation of gene expression —silencing of tumor suppressor genes and enhancing of protooncogenes. There are several tools devoted to the problem of identification of CpG sites' demethylation but majority of them focuses on single site level and does not allow for quantification of region methylation changes. The aim was to create an adaptive algorithm supporting detection of differentially methylated CpG sites and genomic regions specific for acute myeloid leukemia. Knowledge on AML methylation fingerprint helps in better understanding t...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 5, 2018 Category: Bioinformatics Source Type: research

Functional Categorization of Disease Genes Based on Spectral Graph Theory and Integrated Biological Knowledge
AbstractInteraction of multiple genetic variants is a major challenge in the development of effective treatment strategies for complex disorders. Identifying the most promising genes enhances the understanding of the underlying mechanisms of the disease, which, in turn leads to better diagnostic and therapeutic predictions. Categorizing the disease genes into meaningful groups even helps in analyzing the correlated phenotypes which will further improve the power of detecting disease-associated variants. Since experimental approaches are time consuming and expensive, computational methods offer an accurate and efficient alt...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 30, 2018 Category: Bioinformatics Source Type: research

Risk Factors Analysis and Death Prediction in Some Life-Threatening Ailments Using Chi-Square Case-Based Reasoning ( χ 2 CBR) Model
AbstractA wealth of data are available within the health care system, however, effective analysis tools for exploring the hidden patterns in these datasets are lacking. To alleviate this limitation, this paper proposes a simple but promising hybrid predictive model by suitably combining the Chi-square distance measurement with case-based reasoning technique. The study presents the realization of an automated risk calculator and death prediction in some life-threatening ailments using Chi-square case-based reasoning (χ2 CBR) model. The proposed predictive engine is capable of reducing runtime and speeds up execution pro...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 30, 2018 Category: Bioinformatics Source Type: research

Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects
AbstractWhen changes at few amino acid sites are the target of selection, adaptive amino acid changes in protein sequences can be identified using maximum-likelihood methods based on models of codon substitution (such as codeml). Although such methods have been employed numerous times using a variety of different organisms, the time needed to collect the data and prepare the input files means that tens or hundreds of coding regions are usually analyzed. Nevertheless, the recent availability of flexible and easy to use computer applications that collect relevant data (such as BDBM) and infer positively selected amino acid s...
Source: Interdisciplinary Sciences, Computational Life Sciences - January 30, 2018 Category: Bioinformatics Source Type: research