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

miRNA –mRNA Interaction Network in Non-small Cell Lung Cancer
In this study based on paired miRNA and mRNA expression profiles of non-small cell lung cancer samples, we constructed and analyzed miRNA–mRNA interaction network via several bioinformatics softwares and platforms. This integrative network is comprised of 249 nodes for mRNA, 90 nodes for miRNA and 290 edges that show regulations between target genes and miRNAs. The three miR-1207-5p, miR-1228* and miR-939 are the most connected miRNA that regulated a large number of gene s. ST8SIA2, MED1 and HDAC4, SPN, which are targeted by multiple miRNAs and located in the center of the network, are involved in both lung cancer an...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

Computational Modeling of Neuronal Current MRI Signals with Rat Somatosensory Cortical Neurons
In this study, multiple neuronal morphologies of rat tissue were modeled to investigate better estimation of MRI signal change produced by neuronal magnetic field (NMF). Ten pyramidal neurons from layer II to VI of rat somatosensory area with realistic morphology, biophysics, and neuronal density were modeled to simulate NMF of neuronal tissue, from which effects of NMF on MRI signals were obtained. Neuronal current MRI signals, which consist of relative magnitude signal change (RMSC) and phase signal change (PSC), were at least three and one orders of magnitude less than a tissue with single neuron type, respectively. Als...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

Computational Analysis of the Domain Architecture and Substrate-Gating Mechanism of Prolyl Oligopeptidases from Shewanella woodyi and Identification of Probable Lead Molecules
AbstractProlyl oligopeptidases (POPs) are serine proteases found in prokaryotes and eukaryotes which hydrolyze the peptide bond containing proline. The current study focuses on the analysis of POP sequences, their distribution and domain architecture inShewanella woodyi, a Gram-negative, luminous bacterium which causes celiac sprue and similar infections in marine organisms. The POP undergoes huge interdomain movement, which allows possible route for the entry of any substrate. Hence, it offers an opportunity to understand the mechanism of substrate gating by studying the domain architecture and possibility to identify a p...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

In silico Identification of Ergosterol as a Novel Fungal Metabolite Enhancing RuBisCO Activity in Lycopersicum esculentum
AbstractRuBisCO (EC 4.1.1.39), a key enzyme found in stroma of chloroplast, is important for fixing atmospheric CO2 in plants. Alterations in the activity of RuBisCO could influence photosynthetic yield. Therefore, to understand the activity of the protein, knowledge about its structure is pertinent. Though the structure ofNicotiana RuBisCO has been modeled, the structure of tomato RuBisCO is still unknown. RuBisCO extracted from chloroplasts of tomato leaves was subjected to MALDI-TOF –TOF followed by Mascot Search. The protein sequence based on gene identification numbers was subjected to in silico model constructi...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

Discovery of Novel GSK-3 β Inhibitors Using Pharmacophore and Virtual Screening Studies
Abstract Glycogen synthase kinase-3 β (GSK-3β) is a kinase family enzyme and an emerged target for the treatment of various diseases. A total of 23 structurally diverse flavonoid inhibitors were used to generate pharmacophore models using HypoGen algorithm. The hypotheses Hypo1 was considered as a best model which consists of three features: one hydrophobic and two aromatic ring features. The Hypo1 pharmacophore model was employed as a query to screen NCI and natural compound databases to discover novel potential lead compounds. In addition, molecular docking studies were carried out with 596 compounds from scree...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

StressMicrobesInfo: Database of Microorganisms Responsive to Stress Conditions
AbstractMicroorganisms are continuously exposed to numerous stress conditions and had evolved with numerous evolutionary adaptations and physiological acclimation mechanisms against stress effects. Any information related to the microbes responsive to stress conditions will help scientists working in the area of stress biology. Currently, there is lack of information resource on this aspect and for getting information about microbes susceptible or tolerant to different environmental changes, literature searching is the only option. Here, we present a database StressMicrobesInfo that was developed with a mandate to provide ...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

In Silico Study of Variable Surface Proteins in Plasmodium Species: Perspectives in Drug Design
AbstractThe variable surface proteins expressed byP. falciparum andP. vivax are transported to the surface of infected erythrocyte and are exposed to the host immune system. The possibility of using variable surface proteins as a common drug target has been analyzed in both thePlasmodium species. Sequence analysis of variable surface proteins showed a low-level conservation within as well as between the species. Amino acid composition analysis revealed higher frequency of hydrophilic amino acids as compared with that of hydrophobic residues. In order to gain more insight into their diverse functional role, the three-dimens...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

Optimization of the Expression Conditions of CGA-N46 in Bacillus subtilis DB1342(p-3N46) by Response Surface Methodology
AbstractCGA-N46 is a small antifungal-derived peptide and consists of the 31st –76th amino acids of the N-terminus of human chromogranin A. Polycistronic expression of recombinant CGA-N46 inBacillus subtilis DB1342 was used to improve its production, but the yield of CGA-N46 was still low. In the present study, response surface methodology (RSM) was used to optimize culture medium composition and growth conditions of the engineered strainB. subtilis DB1342(p-3N46) for the further increase in CGA-N46 yield. The results of two-level factorial experiments indicated that dextrin and tryptone were significant factors affe...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata : A Molecular Modeling Approach
AbstractSuperoxide dismutases (SODs) act as a first line of the enzymatic antioxidant defense system to control cellular superoxide anion toxicity. Previously, several inhibitors have been widely identified and catalogued for inhibition of SOD activity; however, still the information about the mechanism of interaction and points toward the inhibitor interactions in structures of SODs in general and in extracellular (Ec)-SOD in particular is still in naive. In the present research, we present an insight to elucidate the molecular basis of interactions of SOD inhibitors with Ec-SOD in mud crabScylla serrata using molecular m...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 13, 2016 Category: Bioinformatics Source Type: research

In Silico Molecular Modeling and Docking Studies on Novel Mutants (E229V, H225P and D230C) of the Nucleotide-Binding Domain of Homo sapiens Hsp70
In this study, we explored the possibility of determining the synergistic interactions between nucleotide-binding domain (NBD) ofHomo sapiens heat-shock 70  kDa protein (Hsp70) and E1A 32 kDa of adenovirus serotype 5 motif (PNLVP) in the efficiency of killing of tumor cells in cancer treatment. At present, the protein interaction between NBD and PNLVP motif is still unknown, but believed to enhance the rate of virus replication in tumor cells. Three mutant models (E229V, H225P and D230C) were built and simulated, and their interactions with PNLVP motif were studied. The PNLVP motif showed the binding energy and i...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 12, 2016 Category: Bioinformatics Source Type: research

Structure Prediction of a Novel Exo- β-1,3-Glucanase: Insights into the Cold Adaptation of Psychrophilic Yeast Glaciozyma antarctica PI12
This study elucidates the structural basis of exo-1,3- β-1,3-glucanase from this psychrophilic yeast. The structural prediction of GaExg55 remains a challenge because of its low sequence identity (37 %). A 3D model was constructed for GaExg55. Threading approach was employed to determine a suitable template and generate optimal target–template align ment for establishing the model using MODELLER9v15. The primary sequence analysis of GaExg55 with other mesophilic exo-1,3-β-glucanases indicated that an increased flexibility conferred to the enzyme by a set of amino acids substitutions in the surface and ...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 30, 2016 Category: Bioinformatics Source Type: research

India ’s Computational Biology Growth and Challenges
Abstract India ’s computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to addres s a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinform...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 28, 2016 Category: Bioinformatics Source Type: research

Identification of Novel Abiotic Stress Proteins in Triticum aestivum Through Functional Annotation of Hypothetical Proteins
In this study, an integrated pipeline of software/servers has been used for the identification and functional annotation of 124 unique HPs of T. aestivum considering available data in NCBI till date. All HPs were broadly annotated, out of which functions of 77 HPs were successfully assigned with high confidence level. Precisely functional annotation of remaining 47 HPs is also characterized with low confidence. Several latest versions of protein family databases, pathways information, genomics context methods and in silico tools were utilized to identify and assign function for individual HPs. Annotation result of several ...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 16, 2016 Category: Bioinformatics Source Type: research

Biophysical Studies on HCV 1a NS3/4A Protease and Its Catalytic Triad in Wild Type and Mutants by the In Silico Approach
Abstract The hepatitis C virus (HCV), of the family flaviviridae, is one of the major causes of chronic liver diseases. Until the year 2012, HCV infections were treated using PEG-interferon and ribavirin combinations, which have a low cure rate and severe side effects. Currently, many direct-acting antivirals (DAAs) are available, e.g. protease inhibitors, NS5A and polymerase inhibitors. These drugs have proven to be efficient in interferon-free treatment combinations and capable of enhancing the cure rate to above 90 %. Unlike PEG-interferon and ribavirin combinations, DAAs select for resistance in HCV. The ...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 16, 2016 Category: Bioinformatics Source Type: research

Investigation on Quantitative Structure Activity Relationships of a Series of Inducible Nitric Oxide
Abstract A series of 2-dihydro-4-quinazolin with potent highly selective inhibitors of inducible nitric oxide synthase activities was subjected to quantitative structure activity relationships (QSAR) analysis. Statistically significant equations with high correlation coefficient (r 2 = 0.8219) were developed. The k-nearest neighbor model has showed good cross-validated correlation coefficient and external validation values of 0.7866 and 0.7133, respectively. The selected electrostatic field descriptors the presence of blue ball around R1 and R4 in the quinazolinamine moiety showed electrone...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 6, 2016 Category: Bioinformatics Source Type: research

Implying Analytic Measures for Unravelling Rheumatoid Arthritis Significant Proteins Through Drug –Target Interaction
Abstract Rheumatoid arthritis (RA) is a systemic autoimmune and inflammatory disease that mainly alters the synovial joints and ultimately leads to their destruction. The involvement of the immune system and its related cells is a basic trademark of autoimmune-associated diseases. The present work focuses on network analysis and its functional characterization to predict novel targets for RA. The interactive model called as rheumatoid arthritis drug –target–protein (RA-DTP) is built of 1727 nodes and 7954 edges followed the power-law distribution. RA-DTP comprised of 20 islands, 55 modules and 123 submodules. ...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 1, 2016 Category: Bioinformatics Source Type: research

Flavonoids as Multi-target Inhibitors for Proteins Associated with Ebola Virus: In Silico Discovery Using Virtual Screening and Molecular Docking Studies
Abstract Ebola virus is a single-stranded, negative-sense RNA virus that causes severe hemorrhagic fever in humans and non-human primates. This virus is unreceptive to a large portion of the known antiviral drugs, and there is no valid treatment as on date for disease created by this pathogen. Looking into its ability to create a pandemic scenario across globe, there is an utmost need for new drugs and therapy to combat this life-threatening infection. The current study deals with the evaluation of the inhibitory activity of flavonoids against the four selected Ebola virus receptor proteins, using in silico studi...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 21, 2016 Category: Bioinformatics Source Type: research

A Quantitative Measure of Conformational Changes in Apo, Holo and Ligand-Bound Forms of Enzymes
This study will helps in understanding the level of flexibility in protein–ligand interaction for computer-aided drug designing. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - May 21, 2016 Category: Bioinformatics Source Type: research

Identification of 3-Nitro-2,4,6-trihydroxybenzamide Derivatives as Photosynthetic Electron Transport Inhibitors by QSAR and Pharmacophore Studies
Abstract In the present investigation, quantitative structure–activity relationship (QSAR) analysis was performed on a data set consisting of structurally diverse compounds in order to investigate the role of their structural features on their photosynthetic electron transport Inhibitors. The best 2D-QSAR model was selected, having correlation coefficient r 2 = 0.8544 and cross-validated squared correlation coefficient q 2 = 0.7139 with external predictive ability of pred_r 2 = 0.7753. The results obtained in this study indicate that...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 21, 2016 Category: Bioinformatics Source Type: research

Identify Secretory Protein of Malaria Parasite with Modified Quadratic Discriminant Algorithm and Amino Acid Composition
In this study, the modified method of quadratic discriminant analysis is presented for predicting the secretory proteins. Firstly, 20 amino acids are divided into five types according to the physical and chemical characteristics of amino acids. Then, we used five types of amino acids compositions as inputs of the modified quadratic discriminant algorithm. Finally, the best prediction performance is obtained by using 20 amino acid compositions, the sensitivity of 96 %, the specificity of 92 % with 0.88 of Mathew’s correlation coefficient in fivefold cross-validation test. The results are also compared with t...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 21, 2016 Category: Bioinformatics Source Type: research

Implying Analytic Measures for Unravelling Rheumatoid Arthritis Significant Proteins Through Drug–Target Interaction
Abstract Rheumatoid arthritis (RA) is a systemic autoimmune and inflammatory disease that mainly alters the synovial joints and ultimately leads to their destruction. The involvement of the immune system and its related cells is a basic trademark of autoimmune-associated diseases. The present work focuses on network analysis and its functional characterization to predict novel targets for RA. The interactive model called as rheumatoid arthritis drug–target–protein (RA-DTP) is built of 1727 nodes and 7954 edges followed the power-law distribution. RA-DTP comprised of 20 islands, 55 modules and 123 subm...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 21, 2016 Category: Bioinformatics Source Type: research

TPMT Polymorphism: When Shield Becomes Weakness
Abstract Thiopurine methyltransferase (TPMT) is a cytoplasmic transmethylase present in both prokaryotes and eukaryotes. In humans, it shows its presence in almost all of the tissues, predominantly in liver and kidney. TPMT is one of the important metabolic enzymes of phase II metabolic pathway and catalyzes methylation of thiopurine drugs such as azathioprine, 6-thioguanine and 6-mercaptopurine, which are used to treat patients with neoplasia and autoimmune disease as well as transplant recipients. In this sense, TPMT acts as shield against toxic effect of these drugs. Pharmacogenomic studies revealed that g...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 21, 2016 Category: Bioinformatics Source Type: research

Algorithmic Approach for Removing the Redundancy in Diabetic Gene Categories Based on Semantic Similarity and Gene Expression Data
Abstract Even after so much advancement in gene expression microarray technology, the main hindrance in analyzing microarray data is its limited number of samples as compared to a number of factors, which is a major impediment in revealing actual gene functionality and valuable information from the data. Analyzing gene expression data can indicate the factors which are differentially expressed in the diseased tissue. As most of these genes have no part to play in causing the disease of interest, thus, identification of disease-causing genes can reveal not just the case of the disease, but also its pathogenic mech...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 21, 2016 Category: Bioinformatics Source Type: research

Theoretical Determination of the p K a Values of Betalamic Acid Related to the Free Radical Scavenger Capacity: Comparison Between Empirical and Quantum Chemical Methods
Abstract Health benefits of dietary phytochemicals have been suggested in recent years. Among 1000s of different compounds, Betalains, which occur in vegetables of the Cariophyllalae order (cactus pear fruits and red beet), have been considered because of reducing power and potential to affect redox-modulated cellular processes. The antioxidant power of Betalains is strictly due to the dissociation rate of the acid moieties present in all the molecules of this family of phytochemicals. Experimentally, only the pK a values of betanin were determined. Recently, it was evidenced it was evidenced ...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 21, 2016 Category: Bioinformatics Source Type: research

Identification of Novel Potential gp120 of HIV-1 Antagonist Using Per-Residue Energy Contribution-Based Pharmacophore modelling
This study combines residue energy contribution (REC) pharmacophore mapping of 18A and in silico molecular docking in a virtual screening campaign to identify novel and diverse antagonists of gp120. The binding free energy of a validated docked complex of gp120-18A and the quantitative contribution of interacting residues were obtained with a more accurate molecular mechanics/generalised born surface area (MM/GBSA) method followed by mapping the energetically favourable residue contributions onto atom centres in 18A to obtain a pharmacophore model. The generated pharmacophore hypothesis was used to search the ZINC database...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 10, 2016 Category: Bioinformatics Source Type: research

Molecular Design, Structural Analysis and Antifungal Activity of Derivatives of Peptide CGA-N46
In conclusion, we have successfully identified the active domain of CGA-N46 with strong antifungal activity and weak hemolytic activity, which provides the possibility to develop a new class of antibiotics. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - May 10, 2016 Category: Bioinformatics Source Type: research

Identification of Potential Antituberculosis Drugs Through Docking and Virtual Screening
Abstract Tuberculosis is the most prominent contagious disease and needs the new targets and drugs identification. Target identification and validation is a crucial step in drug discovery process. In Mycobacterium tuberculosis, decaprenyl-phosphoryl-β-d-ribose 2′-oxidase is a potential target for antitubercular chemotherapy. It is encoded by genes dprE1 (Rv3790) and dprE2 (Rv3791). Three-dimensional (3D) structure prediction of selected target (461 amino acid residues) was intent by homology modeling using multitemplate approach based on crystal structure of 2EXR.pdb and 2Q4W.pdb with score = ...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 5, 2016 Category: Bioinformatics Source Type: research

Exploration of Structural and Functional Variations Owing to Point Mutations in α-NAGA
This study computationally explains the underlying reasons for the pathogenesis of the disease, thereby aiding future researchers in drug development and disease management. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - May 2, 2016 Category: Bioinformatics Source Type: research

Online Fault Diagnosis for Biochemical Process Based on FCM and SVM
In this study, a glutamic acid fermentation process is chosen as an example to diagnose the fault by this method, the result shows that the diagnosis time is largely shortened, and the accuracy is extremely improved by comparing to a single SVM method. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - April 29, 2016 Category: Bioinformatics Source Type: research

Binding Patterns Associated Aß-HSP60 p458 Conjugate to HLA-DR-DRB Allele of Human in Alzheimer’s Disease: An In Silico Approach
Abstract Alzheimer’s disease (AD) is a complex, irreversible, progressive brain disorder, which diminishes memory in a slow pace and thinking skills; ranked third by experts. It is a complex disorder that involves numerous cellular and subcellular alterations. The pathogenesis of AD is still unknown, but for better understanding, we proposed an in silico analysis to find out the binding patterns associated with HSP60. Several experimental conclusions have been drawn to understand the actual mechanism behind the forming of aggregation due to misfolding. Protein misfolding disorder is experimentally identified...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 23, 2016 Category: Bioinformatics Source Type: research

Exploration of Novel Human Tyrosinase Inhibitors by Molecular Modeling, Docking and Simulation Studies
Abstract Research studies on human tyrosinase inhibitors and exploration for better cytotoxic agents remain an important line in drug discovery and development at the present time. Recently, multiple inhibitors are being used to cure melanogenesis by targeting human tyrosinase. A series of coumarin (C1–C9)-, thymol (T1–T8)- and vanillin (V1–V8)-based derivatives have been theoretically analyzed for their inhibitory effects against human tyrosinase. The crystal structure of human tyrosinase is not available in Protein Data Bank. Therefore, homology modeling approach was used to predict three-dimen...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 21, 2016 Category: Bioinformatics Source Type: research

In Silico Drug-Designing Studies on Flavanoids as Anticolon Cancer Agents: Pharmacophore Mapping, Molecular Docking, and Monte Carlo Method-Based QSAR Modeling
In conclusion this study have depicted successful and stepwise application of pharmacophore mapping, molecular docking, and QSAR studies in target identification and lead optimization of flavonoids. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - April 8, 2016 Category: Bioinformatics Source Type: research

Transcription Factor Information System (TFIS): A Tool for Detection of Transcription Factor Binding Sites
Abstract Transcription factors are trans-acting proteins that interact with specific nucleotide sequences known as transcription factor binding site (TFBS), and these interactions are implicated in regulation of the gene expression. Regulation of transcriptional activation of a gene often involves multiple interactions of transcription factors with various sequence elements. Identification of these sequence elements is the first step in understanding the underlying molecular mechanism(s) that regulate the gene expression. For in silico identification of these sequence elements, we have developed an online computat...
Source: Interdisciplinary Sciences, Computational Life Sciences - April 6, 2016 Category: Bioinformatics Source Type: research

Flavanoids as Potential NEDD-4 Inhibitors: In Silico Discovery Using Molecular Docking and ADME Studies
Abstract NEDD-4 are closely related E3 ubiquitin-protein ligases that include a C2 domain, three or four WW domains and a catalytic HECT ubiquitin ligase domain. The WW domains of NEDD-4 proteins recognize substrates for ubiquitination by binding the sequence L/PPxY (the PY-motif) present in target proteins. NEDD-4 functions as a suppressor of the epithelial Na+ channel (ENaC), which interacts with NEDD-4 WW domains via PY-motifs located at its C-terminus. Fifty compounds, all of them flavanoids, were subjected to molecular docking studies. The chemical structures were built, and docking studies were done using Sc...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 30, 2016 Category: Bioinformatics Source Type: research

microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations
This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - March 28, 2016 Category: Bioinformatics Source Type: research

StrucBreak: A Computational Framework for Structural Break Detection in DNA Sequences
Abstract Damages or breaks in DNA may change the characteristics of genomes and causes various diseases. In this work we construct a system that incorporates the maximum likelihood-based probabilistic formula to assess the number of damages that have occurred in any DNA sequence. This approach has been progressively benchmarked by implementing simulated data sets so that the outcomes can be compared with a ground truth or reference value. At first the sequence data set order is checked through the statistical cumulative sum (STACUMSUM). The verified sequences are then estimated by prior and posterior probability t...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 28, 2016 Category: Bioinformatics Source Type: research

IWO Algorithm Based on Niche Crowding for DNA Sequence Design
In this study, we specify appropriate constraints that should be satisfied in the design of DNA sequences and we propose evaluation formulae. We employ the Invasive Weed Optimization (IWO) algorithm and the niche crowding in the algorithm to solve the DNA sequence design problem. We also improve the spatial dispersal in the traditional IWO algorithm. Finally, we compared the sequences obtained with existing sequences based on the results obtained using a comprehensive fitness function, which demonstrated the efficiency of the proposed method. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - March 25, 2016 Category: Bioinformatics Source Type: research

From FHB Resistance QTLs to Candidate Genes Identification in Triticum aestivum L.
Abstract Fusarium head blight (FHB) caused by Fusarium graminearum is a worldwide destructive disease affecting cereals such as wheat. FHB resistance is a quantitative trait, and information for FHB resistance QTLs in wheat is available. However, little is known about genes underlying the FHB resistance QTL regions. Using a computational approach in this study, we have mined eight FHB resistance QTLs in wheat and predicted the candidate genes falling within these QTL intervals based on the available sequences and markers. A total of 18 genomic scaffolds located at chromosomes 2AL, 2DL, 3B and 4BS we...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 25, 2016 Category: Bioinformatics Source Type: research

Construction and Identification of the RNAi Recombinant Lentiviral Vector Targeting Human DEPDC7 Gene
In this study, we construct an RNA interference (RNAi) recombinant lentiviral vector particle targeting DEPDC7 in order to knockdown its gene expression in human hepatocellular carcinoma cell line HepG2. We screened three RNAi sequences targeting DEPDC7 and a scramble sequence by the aid of short hairpin RNAs (shRNA) design tools. Then, these sequences were separately cloned into the pLV-H1-EF1α-puro vector to construct four lentiviral vectors (pshRNA-DEPDC7-NC, pshRNA-DEPDC7-RNAi1, pshRNA-DEPDC7-RNAi2 and pshRNA-DEPDC7-RNAi3). All of the recombinant plasmids were identified and confirmed by double digestion and DNA ...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 25, 2016 Category: Bioinformatics Source Type: research

Effect of Solvent Water Molecules on Human Serum Albumin Complex-Docked Paclitaxel by MM-PBSA Method
Abstract Molecular modeling on solvation effect and interaction mechanism of the water molecules in the active site of protein affect significantly the interaction between protein and ligand. Detailed influence of water molecules in the active site of human serum albumin (HSA) on its paclitaxel complex as well as their interaction is essential for clinical studies. Molecular docking of both crystal-HSA and solvated-HSA with paclitaxel was performed in the present work. The docking result shows that paclitaxel is inserted more deeply in the binding pocket of crystal-HSA than in the same site of solvated-HSA, and mo...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 25, 2016 Category: Bioinformatics Source Type: research

Screening of Furanone in Cucurbita melo and Evaluation of its Bioactive Potential Using In Silico Studies
Abstract The work presented here attempts to screen for the presence of 4-Hydroxy-2,5-dimethyl-3(2H)-furanone in fruits and also any bioactive potential present in the fruit extracts. Curcurbita melo was selected for the study, and the fruit was crushed, filtered and extracted with ethyl acetate as the solvent. The resulting extract was subjected to disk diffusion test using Kirby Bauer method for checking its antimicrobial potential. Melon extract showed promising results against different clinical pathogens, 19-mm zone being the largest against Klebsiella pneumoniae and 17 mm against Shigella dysenteriae. G...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 25, 2016 Category: Bioinformatics Source Type: research

Molecular and in Silico Characterization of Achaea janata Granulovirus Granulin Gene
Abstract Achaea janata granulovirus (AcjaGV), an insect virus belonging to Baculoviridae, infects semilooper, a widely distributed defoliating pest on castor beans (Ricinus communis L.) and several other plant hosts in India. The propagation and purification of the Hyderabad isolate AcjaGV were performed, granulin gene from this isolate was amplified, cloned and sequenced, and its homology with other known granulin genes was assessed. The 753-bp granulin ORF of AcjaGV encoded for a granulin protein of 250 amino acids with a molecular mass of 29.5 ± 0.7 kDa. This amino acid sequ...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 16, 2016 Category: Bioinformatics Source Type: research

Molecular Docking and Molecular Dynamics Simulation Studies to Predict Flavonoid Binding on the Surface of DENV2 E Protein
This study demonstrates flavonoids potentially form interactions with the E protein of DENV2. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - March 11, 2016 Category: Bioinformatics Source Type: research

Rising Strengths Hong Kong SAR in Bioinformatics
Abstract Hong Kong’s bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist com...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 9, 2016 Category: Bioinformatics Source Type: research

Insight into the Conformational Variations in SoxYZ Protein Complex from Two Different Members of the β-Proteobacterial Family Involved in Sulfur Oxidation
This study is the first of its kind that analyzes the comparative aspects of the binding interactions of the proteins involved in redox reactions of sulfur anions. This study may, therefore, be helpful in tailoring the microorganisms to function in a better way to remove the environmental sulfur pollutants. Graphical Abstract (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - March 9, 2016 Category: Bioinformatics Source Type: research

Identification of Structurally Diverse Antimicrobials Through Sequential Application of Pharmacophore Modeling, Virtual Screening, Molecular Docking and In Vitro Microbiological Assay
Abstract Dihydrofolate reductase enzyme has been an attractive biological target for the design and development of antimicrobials. Considering this, we have attempted to identify novel dihydrofolate reductase inhibitors through our well-defined in silico and in vitro work flow. An accurate and predictive pharmacophore model comprising of one hydrogen bond acceptor, two hydrophobic and one ring aromatic was developed and utilized as a query to search the National Cancer Institute and Maybridge database leading to retrieval of various compounds which were filtered on the basis of estimated activity, fit value and Li...
Source: Interdisciplinary Sciences, Computational Life Sciences - March 7, 2016 Category: Bioinformatics Source Type: research

Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree ( Olea europaea L.) Cultivars
Abstract The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation ...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 29, 2016 Category: Bioinformatics Source Type: research

Prediction of Phenotypic Effects of Variants Observed in LOC_Os04g36720 of FRO1 Gene in Rice ( Oryza sativa L.)
Abstract In rice, ferric-chelate reductase-1 (FRO1) (LOC_Os04g36720) gene was present on chromosome number 4 and its beginning and ending coordinates where coding sequence lies are 22182599 and 22186943, respectively. It plays a vital role in metal homeostasis and iron transportation in plants. Based on the alignment results, location of single-nucleotide variants is located in open reading frame and their effects of variants were predicted using SIFT sequence tool. The non-synonymous variants at position 342 and 436 lies in helical and coil parts of the protein, respectively, as predicted by Psi-pred server. ...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 17, 2016 Category: Bioinformatics Source Type: research

In Silico Analysis of the Structure of Fungal Fructooligosaccharides-Synthesizing Enzymes
In this study, we present an in silico evaluation of the interactions between substrates (i.e., glucose, sucrose, GF2, GF3, and GF4) and native FOS-synthesizing enzymes from fungi, with reported FOS production yield. In addition, a molecular dynamic simulation was conducted to assess the stability of these interactions. Six fungal enzymes with reported data of FOS production were selected: sucrose–sucrose 1-fructosyltransferase from A. foetidus (GenBank No. CAA04131); intracellular invertase from A. niger (GenBank No. ABB59679); extracellular invertase from A. niger (GenBank No. ABB59678); β-fructofuranidase fro...
Source: Interdisciplinary Sciences, Computational Life Sciences - February 15, 2016 Category: Bioinformatics Source Type: research