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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Sat Dec 01 2007
Journal Name
Electrochimica Acta
Scale-up of a fixed bed electrochemical reactor consisting of parallel screen electrode used for p-aminophenol production
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Publication Date
Sun Dec 01 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Technical requirements for the application of economic intelligence and its impact On the dimensions of strategic success of banks: An applied research on a sample of Iraqi banks private
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This research sheds light on one of the important and vital topics for the banking sectors (technical requirements for the application of economic intelligence) namely by (Hardware, equipment, communication networks, software, databases). And the dimensions of the strategic success of the banks represented by(Customer satisfaction, customer trust, quality of service, growth) In the three Iraqi private banks, namely(Assyria International Investment, Mansour Investment, International Development Investment and Finance). Its implementation is an urgent necessity in order to improve the quality of its banking services to win the satisfaction of its customers and their confidence and then grow to achieve stra

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Publication Date
Tue Dec 31 2019
Journal Name
Journal Of Economics And Administrative Sciences
Determining the sources of growth of the cement industry in Iraq (analytical study for the period 1990-2014)
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The objective of this study is to determine the sources of growth of the cement industry in Iraq for the period 1990-2014 and to indicate the nature of the technological progress used in it. To achieve this objective we have built an econometric model, by adapting the production function constant elasticity for substitution, using multiple regression, and enforcement, SPSS program, and using the ordinary least squares method (OLS). The results showed that quantitative factors (labour and capital) are the main sources of growth the cement industry in Iraq, and the qualitative factors (technological progress) did not contribute effectively to achieve this growth. And that the production techniques adopted in the cement industry in

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Publication Date
Mon Oct 09 2023
Journal Name
Nasaq
A Critical Formalistic Reading in Emily Dickinson’s I felt a Funeral, in my Brain and T.S.Eliot’s The Love Song of J. Alfred Prufrock
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A CRITICAL OVERVIEW IN SELECTED POEMS

Publication Date
Sat Sep 01 2007
Journal Name
Al-khwarizmi Engineering Journal
Free Convective Heat Transfer with Different Sections Lengths Placed at the Exit of a Vertical Circular Tube subjected to a Constant Heat Flux
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A free convective heat transfer from the inside surface of a uniformly heated vertical circular tube has been experimentally investigated under a constant wall heat flux boundary condition for laminar air flow in the ranges of RaL from 6.9108 to 5109. The effect of the different sections (restrictions) lengths placed at the exit of the heated tube on the surface temperature distribution, the local and average heat transfer coefficients were examined. The experimental apparatus consists of aluminum circular tube with 900 mm length and 30 mm inside diameter (L/D=30). The exit sections (restrictions) were included circular tubes having the same inside diameter as the heated tube but with different lengths of

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Synthesis and Spectroscopic Characterization for Some Metal ion Complexes with 2-Hydroxy-3-((5-Mercapto-1,3,4-Thiadiazol-2-yl)Diazenyl)-1-Naphthaldehyde
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New metal ion complexes were synthesized with the general formula; K[PtLCl4], [ReLCl4] and K[ML(Cl)2] where M = Pd(II), Cd(II), Zn(II) and Hg(II), from the Azo ligand (HL) [2-Hydroxy-3-((5-mercapto-1,3,4-thiadiazol-2-yl)diazenyl)-1-naphth aldehyde] (HL) the ligand was synthesized from (2-hydroxy-1-naphthaldehyde) and (5-amino-1,3,4-thiadiazole-2-thiol). The ligand and its metal complexes are characterized by phisco- chemical spectroscopic techniques (FT.IR, UV-Vis and Mass spectra, elemental analysis, molar conductivity, Atomic Absorption, Chloride contain and magnetic susceptibility). The spectral data suggest that the (HL) behaves as a bidentate ligand in all complexes. These studies revealed tetrahedral geometries for all metal complexes

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Publication Date
Fri Sep 30 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Kinetic Study of Transesterification Reaction of Edible Oil Using Heterogenous Catalyst
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AlPO4 solid acid catalyst was prepared in order to use it in transesterification reaction of edible oil after supporting it with tungsten oxide. The maximum conversion of edible oil was obtained 78.78% at catalyst concentration (5gm.), temperature 70°Ϲ, 30/1 methanol/edible oil molar ratio, and time 5hr. The study of kinetics of the transesterification reaction of edible oil indicates that the reaction has an order of 3/2, while the value of activation energy for  transesterification reaction is 51.367 kJ/mole and frequency factor equal 26219.13(L/ mol.minute).

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Publication Date
Fri Sep 30 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Kinetic Study of Transesterification Reaction of Edible Oil Using Heterogenous Catalyst
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   AlPO4 solid acid catalyst was prepared in order to use it in transesterification reaction of edible oil after supporting it with tungsten oxide. The maximum conversion of edible oil was obtained 78.78% at catalyst concentration (5gm.), temperature 70°Ϲ, 30/1 methanol/edible oil molar ratio, and time 5hr. The study of kinetics of the transesterification reaction of edible oil indicates that the reaction has an order of 3/2, while the value of activation energy for  transesterification reaction is 51.367 kJ/mole and frequency factor equal 26219.13(L/ mol.minute).

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Publication Date
Mon Feb 04 2019
Journal Name
Iraqi Journal Of Physics
Environmental study of groundwater in southwest of Baghdad, Yusufiyah using GIS
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Ground water hydrochemical study in Yusufiyah depends upon (25) wells where major cations and anions were obtained as well as trace elements. The hydrochemical properties include the study of (pH, EC, TDS, and TH). The groundwater of the study area is odorless and colorless except the wells (13 and 16) with a salty taste due to the elevated (TDS) concentration in it, where the wells depth ranges between 7-20 meters. Depth of water in these wells was about 25-35 meters above sea level. Groundwater generally flows from east to west and from north east to south west. The resource of groundwater depends upon surface water. Physical specifications are measured in the water samples included temperature, color, taste, odor, pH, electrical condu

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Publication Date
Fri Oct 12 2018
Journal Name
International Journal Of Dynamics And Control
Decentralized adaptive partitioned approximation control of high degrees-of-freedom robotic manipulators considering three actuator control modes
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