Search results for: energy based approach;binding sites
15757 Identification and Analysis of Binding Site Residues in Protein-Protein Complexes
Authors: M. Michael Gromiha, Kiyonobu Yokota, Kazuhiko Fukui
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We have developed an energy based approach for identifying the binding sites and important residues for binding in protein-protein complexes. We found that the residues and residuepairs with charged and aromatic side chains are important for binding. These residues influence to form cation-¤Ç, electrostatic and aromatic interactions. Our observation has been verified with the experimental binding specificity of protein-protein complexes and found good agreement with experiments. The analysis on surrounding hydrophobicity reveals that the binding residues are less hydrophobic than non-binding sites, which suggests that the hydrophobic core are important for folding and stability whereas the surface seeking residues play a critical role in binding. Further, the propensity of residues in the binding sites of receptors and ligands, number of medium and long-range contacts, and influence of neighboring residues will be discussed.
Keywords: Protein-protein interactions, energy based approach;binding sites, propensity, long-range contacts, hydrophobicity
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 138715756 Intragenic MicroRNAs Binding Sites in MRNAs of Genes Involved in Carcinogenesis
Authors: Olga A. Berillo, Assel S. Issabekova, Anatoly T. Ivashchenko
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MiRNAs participate in gene regulation of translation. Some studies have investigated the interactions between genes and intragenic miRNAs. It is important to study the miRNA binding sites of genes involved in carcinogenesis. RNAHybrid 2.1 and ERNAhybrid programmes were used to compute the hybridization free energy of miRNA binding sites. Of these 54 mRNAs, 22.6%, 37.7%, and 39.7% of miRNA binding sites were present in the 5'UTRs, CDSs, and 3'UTRs, respectively. The density of the binding sites for miRNAs in the 5'UTR ranged from 1.6 to 43.2 times and from 1.8 to 8.0 times greater than in the CDS and 3'UTR, respectively. Three types of miRNA interactions with mRNAs have been revealed: 5'- dominant canonical, 3'-compensatory, and complementary binding sites. MiRNAs regulate gene expression, and information on the interactions between miRNAs and mRNAs could be useful in molecular medicine. We recommend that newly described sites undergo validation by experimental investigation.Keywords: Exon, intron, miRNA, oncogene.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 199715755 MiRNAs as Regulators of Tumour Suppressor Expression
Authors: Olga A. Berillo, Gaukhar K. Baidildinova, Аnatoliy Т. Ivashchenko
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Tumour suppressors are key participants in the prevention of cancer. Regulation of their expression through miRNAs is important for comprehensive translation inhibition of tumour suppressors and elucidation of carcinogenesis mechanisms. We studies the possibility of 1521 miRNAs to bind with 873 mRNAs of human tumour suppressors using RNAHybrid 2.1 and ERNAhybrid programmes. Only 978 miRNAs were found to be translational regulators of 812 mRNAs, and 61 mRNAs did not have any miRNA binding sites. Additionally, 45.9% of all miRNA binding sites were located in coding sequences (CDSs), 33.8% were located in 3' untranslated region (UTR), and 20.3% were located in the 5'UTR. MiRNAs binding with more than 50 target mRNAs and mRNAs binding with several miRNAs were selected. Hsa-miR-5096 had 15 perfectly complementary binding sites with mRNAs of 14 tumour suppressors. These newly indentified miRNA binding sites can be used in the development of medicines (anti-sense therapies) for cancer treatment.Keywords: Exonic miRNA, intergenic miRNA, intronic miRNA, tumor suppressor.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 182415754 Introducing Sequence-Order Constraint into Prediction of Protein Binding Sites with Automatically Extracted Templates
Authors: Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu, Darby Tien-Hao Chang
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Search for a tertiary substructure that geometrically matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work, a web server has been built to predict protein-ligand binding sites based on automatically extracted templates. However, a drawback of such templates is that the web server was prone to resulting in many false positive matches. In this study, we present a sequence-order constraint to reduce the false positive matches of using automatically extracted templates to predict protein-ligand binding sites. The binding site predictor comprises i) an automatically constructed template library and ii) a local structure alignment algorithm for querying the library. The sequence-order constraint is employed to identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequence-order constraint can largely reduce the false positive matches and is effective for template-based binding site prediction.Keywords: Protein structure, binding site, functional prediction
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 145515753 Binding of miR398 to mRNA of Chaperone and Superoxide Dismutase Genes in Plants
Authors: Assyl Bari, Olga Berillo, Saltanat Orazova, Anatoliy Ivashchenko
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Among all microRNAs (miRNAs) in 12 plant species investigated in this study, only miR398 targeted the copper chaperone for superoxide dismutase (CCS). The nucleotide sequences of miRNA binding sites were located in the mRNA protein-coding sequence (CDS) and were highly homologous. These binding sites in CCS mRNA encoded a conservative GDLGTL hexapeptide. The binding sites for miR398 in the CDS of superoxide dismutase 1 mRNA encoded GDLGN pentapeptide. The conservative miR398 binding site located in the CDS of superoxide dismutase 2 mRNA encoded the GDLGNI hexapeptide. The miR398 binding site in the CDS of superoxide dismutase 3 mRNA encoded the GDLGNI or GDLGNV hexapeptide. Gene expression of the entire superoxide dismutase family in the studied plant species was regulated only by miR398. All members of the miR398 family, i.e. miR398a,b,c were connected to one site for each CuZnSOD and chaperone mRNA.
Keywords: MicroRNA, mRNA, plant, superoxide dismutase.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 189715752 Crystalline Model Approach for Studying the Nuclear Properties of Light Nuclei
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A study of the structure of the nucleus with the analogy by solid-state physics has been developed. We have used binding energy to calculate R (a parameter that is proportional to the radius of the nucleus) for deuteron, alpha, and 8Be. The calculated parameter r calculated from solid state physics produces a probe for calculation the nuclear radii. 8Be has special attention as it is radioactive nucleus and the latest nucleus to be calculated from crystalline model approach. The distribution of nucleons inside the nucleus is taken to be tetrahedral for 16O. The model has failed to expect the radius of 9Be which is an impression about the modification should be done on the model at near future. A comparison between our calculations and those from literature has been made, and a good agreement has been obtained.
Keywords: The structure of the nucleus, binding energy, crystalline model approach, nuclear radii, tetrahedral for 16O.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 48615751 Dynamic Bus Binding for Low Power Using Multiple Binding Tables
Authors: Jihyung Kim, Taejin Kim, Sungho Park, Jun-Dong Cho
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A conventional binding method for low power in a high-level synthesis mainly focuses on finding an optimal binding for an assumed input data, and obtains only one binding table. In this paper, we show that a binding method which uses multiple binding tables gets better solution compared with the conventional methods which use a single binding table, and propose a dynamic bus binding scheme for low power using multiple binding tables. The proposed method finds multiple binding tables for the proper partitions of an input data, and switches binding tables dynamically to produce the minimum total switching activity. Experimental result shows that the proposed method obtains a binding solution having 12.6-28.9% smaller total switching activity compared with the conventional methods.Keywords: low power, bus binding, switching activity, multiplebinding tables
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 117615750 Critical Assessment of Scoring Schemes for Protein-Protein Docking Predictions
Authors: Dhananjay C. Joshi, Jung-Hsin Lin
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Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.
Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 179115749 Computational Studies of Binding Energies and Structures of Methylamine on Functionalized Activated Carbon Surfaces
Authors: R. C. J. Mphahlele, K. Bolton, H. Kasaini
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Empirical force fields and density functional theory (DFT) was used to study the binding energies and structures of methylamine on the surface of activated carbons (ACs). This is a first step in studying the adsorption of alkyl amines on the surface of functionalized ACs. The force fields used were Dreiding (DFF), Universal (UFF) and Compass (CFF) models. The generalized gradient approximation with Perdew Wang 91 (PW91) functional was used for DFT calculations. In addition to obtaining the aminecarboxylic acid adsorption energies, the results were used to establish reliability of the empirical models for these systems. CFF predicted a binding energy of -9.227 (kcal/mol) which agreed with PW91 at - 13.17 (kcal/mol), compared to DFF 0 (kcal/mol) and UFF -0.72 (kcal/mol). However, the CFF binding energies for the amine to ester and ketone disagreed with PW91 results. The structures obtained from all models agreed with PW91 results.Keywords: Activated Carbons, Binding energy, DFT, Force fields.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 193615748 Low Power Bus Binding Based on Dynamic Bit Reordering
Authors: Jihyung Kim, Taejin Kim, Sungho Park, Jun-Dong Cho
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In this paper, the problem of reducing switching activity in on-chip buses at the stage of high-level synthesis is considered, and a high-level low power bus binding based on dynamic bit reordering is proposed. Whereas conventional methods use a fixed bit ordering between variables within a bus, the proposed method switches a bit ordering dynamically to obtain a switching activity reduction. As a result, the proposed method finds a binding solution with a smaller value of total switching activity (TSA). Experimental result shows that the proposed method obtains a binding solution having 12.0-34.9% smaller TSA compared with the conventional methods.Keywords: bit reordering, bus binding, low power, switching activity matrix
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 129415747 Novel Inhibitor of E. coli DNA Adenine Methyltransferase (Ecodam)
Authors: H. Elsawy, A. Jeltsch
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EcoDam is an adenine-N6 DNA methyltransferase that methylates the GATC sites in the Escherichia coli genome. DNA-adenine methylation is not present in higher eukaryotes including humans. These observations raise the possibility that dam inhibitors may be used as anti-microbial agents. Polyphosphate (Poly(P)) is an important metabolite and signaling molecule in prokaryotes and eukaryotes. Here, by using gel retardation experiments to investigate the competition of DNA binding by EcoDam in the presence of polyphosphate, we found that Poly (P) strongly interferes with DNA binding by EcoDam, while same concentration of monophosphate does not. In addition, we demonstrated that Poly (P) binding inhibits the activity of EcoDam and our results suggest that Poly (P) led to strong inhibition of the EcoDam catalytic activity, while monophosphate had only moderate effect.Keywords: Antibacterial drugs, EcoDam inhibitors, Polyphosphate.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 255315746 Prediction of Binding Free Energies for Dyes Removal Using Computational Chemistry
Authors: R. Chanajaree, D. Luanwiset, K. Pongpratea
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Dye removal is an environmental concern because the textile industries have been increasing by world population and industrialization. Adsorption is the technique to find adsorbents to remove dyes from wastewater. This method is low-cost and effective for dye removal. This work tries to develop effective adsorbents using the computational approach because it will be able to predict the possibility of the adsorbents for specific dyes in terms of binding free energies. The computational approach is faster and cheaper than the experimental approach in case of finding the best adsorbents. All starting structures of dyes and adsorbents are optimized by quantum calculation. The complexes between dyes and adsorbents are generated by the docking method. The obtained binding free energies from docking are compared to binding free energies from the experimental data. The calculated energies can be ranked as same as the experimental results. In addition, this work also shows the possible orientation of the complexes. This work used two experimental groups of the complexes of the dyes and adsorbents. In the first group, there are chitosan (adsorbent) and two dyes (reactive red (RR) and direct sun yellow (DY)). In the second group, there are poly(1,2-epoxy-3-phenoxy) propane (PEPP), which is the adsorbent, and 2 dyes of bromocresol green (BCG) and alizarin yellow (AY).
Keywords: Dye removal, binding free energies, quantum calculation, docking.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 70715745 Extended Low Power Bus Binding Combined with Data Sequence Reordering
Authors: Jihyung Kim, Taejin Kim, Sungho Park, Jun-Dong Cho
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In this paper, we address the problem of reducing the switching activity (SA) in on-chip buses through the use of a bus binding technique in high-level synthesis. While many binding techniques to reduce the SA exist, we present yet another technique for further reducing the switching activity. Our proposed method combines bus binding and data sequence reordering to explore a wider solution space. The problem is formulated as a multiple traveling salesman problem and solved using simulated annealing technique. The experimental results revealed that a binding solution obtained with the proposed method reduces 5.6-27.2% (18.0% on average) and 2.6-12.7% (6.8% on average) of the switching activity when compared with conventional binding-only and hybrid binding-encoding methods, respectively.Keywords: low power, bus binding, switching activity, multiple traveling salesman problem, data sequence reordering
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 132315744 In silico Studies on Selected Drug Targets for Combating Drug Resistance in Plasmodium falcifarum
Authors: D. Bhaskar, N. R. Wadehra, M. Gulati, A. Narula, R. Vishnu, G. Katyal
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With drug resistance becoming widespread in Plasmodium falciparum infections, the development of the alternative drugs is the desired strategy for prevention and cure of malaria. Three drug targets were selected to screen promising drug molecules from the GSK library of 13469 molecules. Using an in silico structure-based drug designing approach, the differences in binding energies of the substrate and inhibitor were exploited between target sites of parasite and human to design a drug molecule against Plasmodium. The docking studies have shown several promising molecules from GSK library with more effective binding as compared to the already known inhibitors for the drug targets. Though stronger interaction has been shown by several molecules as compared to the reference, few molecules have shown the potential as drug candidates though in vitro studies are required to validate the results. In case of thymidylate synthase-dihydrofolatereductase (TS-DHFR), three compounds have shown promise for future studies as potential drugs.
Keywords: Drug resistance, Drug targets, In silico studies, Plasmodium falciparum.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 192615743 An Approximation Method for Three Quark Systems in the Hyper-Spherical Approach
Authors: B. Rezaei, G. R. Boroun, M. Abdolmaleki
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The bound state energy of three quark systems is studied in the framework of a non- relativistic spin independent phenomenological model. The hyper- spherical coordinates are considered for the solution this system. According to Jacobi coordinate, we determined the bound state energy for (uud) and (ddu) quark systems, as quarks are flavorless mass, and it is restrict that choice potential at low and high range in nucleon bag for a bound state.
Keywords: Adiabatic expansion, grand angular momentum, binding energy, perturbation, baryons.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 142215742 Characteristics of Intronic and Intergenic Human miRNAs and Features of their Interaction with mRNA
Authors: Assel S. Issabekova, Olga A. Berillo, Vladimir A. Khailenko, Shara A. Atambayeva, Mireille Regnier, Anatoly T. Ivachshenko
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Regulatory relationships of 686 intronic miRNA and 784 intergenic miRNAs with mRNAs of 51 intronic miRNA coding genes were established. Interaction features of studied miRNAs with 5'UTR, CDS and 3'UTR of mRNA of each gene were revealed. Functional regions of mRNA were shown to be significantly heterogenous according to the number of binding sites of miRNA and to the location density of these sites.
Keywords: 5'UTR, 3'UTR, CDS, miRNA, target mRNA
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 169415741 Metal-Based Anticancer Agents: In vitro DNA Binding, Cleavage and Cytotoxicity
Authors: Mala Nath, Nagamani Kompelli, Partha Roy, Snehasish Das
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Two new metal-based anticancer chemotherapeutic agents, [(Ph2Sn)2(HGuO)2(phen)Cl2] 1 and [(Ph3Sn)(HGuO)(phen)]- Cl.CH3OH.H2O 2, were designed, prepared and characterized by analytical and spectral (IR, ESI-Mass, 1H, 13C and 119Sn NMR) techniques. The proposed geometry of Sn(IV) in 1 and 2 is distorted octahedral and distorted trigonal-bipyramidal, respectively. Both 1 and 2 exhibit potential cytotoxicity in vitro against MCF-7, HepG-2 and DU-145 cell lines. The intrinsic binding constant (Kb) values of 1 (2.33 × 105 M-1) and 2 (2.46 × 105 M-1) evaluated from UV-Visible absorption studies suggest non-classical electrostatic mode of interaction via phosphate backbone of DNA double helix. The Stern- Volmer quenching constant (Ksv) of 1 (9.74 × 105 M-1) and 2 (2.9 × 106 M-1) determined by fluorescence studies suggests the groove binding and intercalation mode for 1 and 2, respectively. Effective cleavage of pBR322 DNA is induced by 1.Their interaction with DNA of cancer cells may account for potency.
Keywords: Anticancer agents, DNA binding studies, NMR spectroscopy, organotin.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 276715740 The Influence of Physical-Mechanical and Thermal Properties of Hemp Filling Materials by the Addition of Energy Byproducts
Authors: Sarka Keprdova, Jiri Bydzovsky
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This article describes to what extent the addition of energy by-products into the structures of the technical hemp filling materials influence their properties. The article focuses on the changes in physical-mechanical and thermal technical properties of materials after the addition of ash or FBC ash or slag in the binding component of material. Technical hemp filling materials are made of technical hemp shives bonded by the mixture of cement and dry hydrate lime. They are applicable as fillers of vertical or horizontal structures or roofs. The research used eight types of energy by-products of power or heating plants in the Czech Republic. Secondary energy products were dispensed in three different percentage ratios as a replacement of cement in the binding component. Density, compressive strength and determination of the coefficient of thermal conductivity after 28, 60 and 90 days of curing in a laboratory environment were determined and subsequently evaluated on the specimens produced.
Keywords: Ash, binder, cement, energy by-product, FBC ash (fluidized bed combustion ash), filling materials, shives, slag, technical hemp.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 188715739 Systematic Approach for Energy-Supply-Orientated Production Planning
Authors: F. Keller, G. Reinhart
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The efficient and economic allocation of resources is one main goal in the field of production planning and control. Nowadays, a new variable gains in importance throughout the planning process: Energy. Energy-efficiency has already been widely discussed in literature, but with a strong focus on reducing the overall amount of energy used in production. This paper provides a brief systematic approach, how energy-supply-orientation can be used for an energy-cost-efficient production planning and thus combining the idea of energy-efficiency and energy-flexibility.Keywords: Production planning and control, energy, efficiency, flexibility.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 161315738 Clustering in WSN Based on Minimum Spanning Tree Using Divide and Conquer Approach
Authors: Uttam Vijay, Nitin Gupta
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Due to heavy energy constraints in WSNs clustering is an efficient way to manage the energy in sensors. There are many methods already proposed in the area of clustering and research is still going on to make clustering more energy efficient. In our paper we are proposing a minimum spanning tree based clustering using divide and conquer approach. The MST based clustering was first proposed in 1970’s for large databases. Here we are taking divide and conquer approach and implementing it for wireless sensor networks with the constraints attached to the sensor networks. This Divide and conquer approach is implemented in a way that we don’t have to construct the whole MST before clustering but we just find the edge which will be the part of the MST to a corresponding graph and divide the graph in clusters there itself if that edge from the graph can be removed judging on certain constraints and hence saving lot of computation.
Keywords: Algorithm, Clustering, Edge-Weighted Graph, Weighted-LEACH.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 245415737 Fluorescence Spectroscopy of Lysozyme-Silver Nanoparticles Complex
Authors: S. Ashrafpour, T. Tohidi Moghadam, B. Ranjbar
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Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 μM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme- AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.
Keywords: Nanocarrier, Nanoparticles, Surface Plasmon Resonance, Quenching Fluorescence.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 256015736 Computational Design of Inhibitory Agents of BMP-Noggin Interaction to Promote Osteogenesis
Authors: Shaila Ahmed, Raghu Prasad Rao Metpally, Sreedhara Sangadala, Boojala Vijay B Reddy
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Bone growth factors, such as Bone Morphogenic Protein-2 (BMP-2) have been approved by the FDA to replace grafting for some surgical interventions, but the high dose requirement limits its use in patients. Noggin, an extracellular protein, blocks the effect of BMP-2 by binding to BMP. Preventing the BMP-2/noggin interaction will help increase the free concentration of BMP-2 and therefore should enhance its efficacy to induce bone formation. The work presented here involves computational design of novel small molecule inhibitory agents of BMP-2/noggin interaction, based on our current understanding of BMP-2, and its known putative ligands (receptors and antagonists). A successful acquisition of such an inhibitory agent of BMP-2/noggin interaction would allow clinicians to reduce the dose required of BMP-2 protein in clinical applications to promote osteogenesis. The available crystal structures of the BMPs, its receptors, and the binding partner noggin were analyzed to identify the critical residues involved in their interaction. In presenting this study, LUDI de novo design method was utilized to perform virtual screening of a large number of compounds from a commercially available library against the binding sites of noggin to identify the lead chemical compounds that could potentially block BMP-noggin interaction with a high specificity.Keywords: Transforming growth factor-beta, Bone morphogenic proteins, Noggin, LUDI de novo design method, CAP small molecules.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 191015735 Interaction of Low-Energy Positrons with Mg Atoms: Elastic Scattering, Bound States, and Annihilation
Authors: Mahasen M. Abdel-Mageed, H. S. Zaghloul
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Annihilations, phase shifts, scattering lengths and elastic cross sections of low energy positrons scattering from magnesium atoms were studied using the least-squares variational method (LSVM). The possibility of positron binding to the magnesium atoms is investigated. A trial wave function is suggested to represent e+-Mg elastic scattering and scattering parameters were derived to estimate the binding energy and annihilation rates. The trial function is taken to depend on several adjustable parameters, and is improved iteratively by increasing the number of terms. The present results have the same behavior as reported semi-empirical, theoretical and experimental results. Especially, the estimated positive scattering length supports the possibility of positronmagnesium bound state system that was confirmed in previous experimental and theoretical work.Keywords: Bound wave function, Positron Annihilation, scattering phase shift, scattering length.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 117715734 Techno-Economic Analysis Framework for Wave Energy Conversion Schemes under South African Conditions: Modeling and Simulations
Authors: Siyanda S. Biyela, Willie A. Cronje
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This paper presents a desktop study of comparing two different wave energy to electricity technologies (WECs) using a techno-economic approach. This techno-economic approach forms basis of a framework for rapid comparison of current and future technologies. The approach also seeks to assist in investment and strategic decision making expediting future deployment of wave energy harvesting in South Africa.Keywords: Cost of energy, tool, wave energy converter, WEC-Sim.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 119215733 Molecular Mechanism of Amino Acid Discrimination for the Editing Reaction of E.coli Leucyl-tRNA Synthetase
Authors: Keun Woo Lee, Minky Son, Chanin Park, Ayoung Baek
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Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.
Keywords: Amino acid discrimination, Binding free energy Leucyl-tRNAsynthetase, Molecular dynamics.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 163215732 Energy Map Construction using Adaptive Alpha Grey Prediction Model in WSNs
Authors: Surender Kumar Soni, Dhirendra Pratap Singh
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Wireless Sensor Networks can be used to monitor the physical phenomenon in such areas where human approach is nearly impossible. Hence the limited power supply is the major constraint of the WSNs due to the use of non-rechargeable batteries in sensor nodes. A lot of researches are going on to reduce the energy consumption of sensor nodes. Energy map can be used with clustering, data dissemination and routing techniques to reduce the power consumption of WSNs. Energy map can also be used to know which part of the network is going to fail in near future. In this paper, Energy map is constructed using the prediction based approach. Adaptive alpha GM(1,1) model is used as the prediction model. GM(1,1) is being used worldwide in many applications for predicting future values of time series using some past values due to its high computational efficiency and accuracy.Keywords: Adaptive Alpha GM(1, 1) Model, Energy Map, Prediction Based Data Reduction, Wireless Sensor Networks
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 179215731 Forecasting Direct Normal Irradiation at Djibouti Using Artificial Neural Network
Authors: Ahmed Kayad Abdourazak, Abderafi Souad, Zejli Driss, Idriss Abdoulkader Ibrahim
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In this paper Artificial Neural Network (ANN) is used to predict the solar irradiation in Djibouti for the first Time that is useful to the integration of Concentrating Solar Power (CSP) and sites selections for new or future solar plants as part of solar energy development. An ANN algorithm was developed to establish a forward/reverse correspondence between the latitude, longitude, altitude and monthly solar irradiation. For this purpose the German Aerospace Centre (DLR) data of eight Djibouti sites were used as training and testing in a standard three layers network with the back propagation algorithm of Lavenber-Marquardt. Results have shown a very good agreement for the solar irradiation prediction in Djibouti and proves that the proposed approach can be well used as an efficient tool for prediction of solar irradiation by providing so helpful information concerning sites selection, design and planning of solar plants.Keywords: Artificial neural network, solar irradiation, concentrated solar power, Lavenberg-Marquardt.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 106715730 A Rough Sets Approach for Relevant Internet/Web Online Searching
Authors: Erika Martinez Ramirez, Rene V. Mayorga
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The internet is constantly expanding. Identifying web links of interest from web browsers requires users to visit each of the links listed, individually until a satisfactory link is found, therefore those users need to evaluate a considerable amount of links before finding their link of interest; this can be tedious and even unproductive. By incorporating web assistance, web users could be benefited from reduced time searching on relevant websites. In this paper, a rough set approach is presented, which facilitates classification of unlimited available e-vocabulary, to assist web users in reducing search times looking for relevant web sites. This approach includes two methods for identifying relevance data on web links based on the priority and percentage of relevance. As a result of these methods, a list of web sites is generated in priority sequence with an emphasis of the search criteria.Keywords: Web search, Web Mining, Rough Sets, Web Intelligence, Intelligent Portals, Relevance.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 154415729 Energy Production from Marine Biomass: Fuel Cell Power Generation Driven by Methane Produced from Seaweed
Authors: Shinya Yokoyama, Katsunari Jonouchi, Kenji Imou
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This paper discusses the utilization of marine biomass as an energy resource in Japan. A marine biomass energy system in Japan was proposed consisting of seaweed cultivation (Laminaria japonica) at offshore marine farms, biogas production via methane fermentation of the seaweeds, and fuel cell power generation driven by the generated biogas. We estimated energy output, energy supply potential, and CO2 mitigation in Japan on the basis of the proposed system. As a result, annual energy production was estimated to be 1.02-109 kWh/yr at nine available sites. Total CO2 mitigation was estimated to be 1.04-106 tonnes per annum at the nine sites. However, the CO2 emission for the construction of relevant facilities is not taken into account in this paper. The estimated CO2 mitigation is equivalent to about 0.9% of the required CO2 mitigation for Japan per annum under the Kyoto Protocol framework.Keywords: CO2 mitigation, Fuel cell power generation, Laminaria japonica, Marine biomass, Seaweed.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 472815728 Computer Aided Docking Studies on Antiviral Drugs for SARS
Authors: Virupakshaiah DBM, Chandrakanth Kelmani, Rachanagouda Patil, Prasad Hegade
Abstract:
Severe acute respiratory syndrome (SARS) is a respiratory disease in humans which is caused by the SARS coronavirus. The treatment of coronavirus-associated SARS has been evolving and so far there is no consensus on an optimal regimen. The mainstream therapeutic interventions for SARS involve broad-spectrum antibiotics and supportive care, as well as antiviral agents and immunomodulatory therapy. The Protein- Ligand interaction plays a significant role in structural based drug designing. In the present work we have taken the receptor Angiotensin converting enzyme 2 and identified the drugs that are commonly used against SARS. They are Lopinavir, Ritonavir, Ribavirin, and Oseltamivir. The receptor Angiotensin converting enzyme 2 (ACE-2) was docked with above said drugs and the energy value obtained are as follows, Lopinavir (-292.3), Ritonavir (-325.6), Oseltamivir (- 229.1), Ribavirin (-208.8). Depending on the least energy value we have chosen the best two drugs out of the four conventional drugs. We tried to improve the binding efficiency and steric compatibility of the two drugs namely Ritonavir and Lopinavir. Several modifications were made to the probable functional groups (phenylic, ketonic groups in case of Ritonavir and carboxylic groups in case of Lopinavir respectively) which were interacting with the receptor molecule. Analogs were prepared by Marvin Sketch software and were docked using HEX docking software. Lopinavir analog 8 and Ritonavir analog 11 were detected with significant energy values and are probable lead molecule. It infers that some of the modified drugs are better than the original drugs. Further work can be carried out to improve the steric compatibility of the drug based upon the work done above for a more energy efficient binding of the drugs to the receptor.
Keywords: Protein data bank, Rasmol, Marvin sketch, Hexdocking.
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