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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
Tue Nov 29 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A proposed form for the Combined Assurance report and its impact In achieving sustainable development in the Iraqi economic units
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Despite the importance of sustainable development and its dimensions in developing performance and supporting competitive advantage in economic units, there is a gap and lack of coordination between Combined Assurance  providers (management, internal audit, external audit) to report on sustainable development, and the research aims to propose a model for the Combined Assurance report to achieve development sustainable development in the Iraqi economic units, especially the Baghdad Municipality, enables assurance providers to coordinate efforts that lead to the achievement of Combined Assurance, The research found the proposed model for the Combined Assurance report in achieving sustainable development in the Iraqi economic units, es

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Publication Date
Fri Jan 21 2022
Journal Name
International Journal Of Research In Social Sciences And Humanities
Managing Trading Decisions Using The True Strength Index –An Applied Study
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The purpose of this research is to test the ability of the true strength index To time and manage trading in the financial market to select the best stocks and achieve a higher return than the Simple buy and hold strategy. And To achieve the objectives of the research, it relied on the main hypothesis, which is By using the True Strength Index to manage trading decisions buying and selling, can be achieved higher returns than the buy and hold strategy . The research community has been identified with all stocks listed on the Iraq Stock Exchange. Implementing the financial research tests requires selecting a sample from the research community that fulfills the test requirements according to a number of conditions So (38) companies we

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Publication Date
Thu Dec 31 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Electrolytic removal of zinc from simulated chloride wastewaters using a novel flow-by fixed bed electrochemical reactor
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The cathodic deposition of zinc from simulated chloride wastewater was used to characterize the mass transport properties of a flow-by fixed bed electrochemical reactor composed of vertical stack  of stainless steel nets, operated in batch-recycle mode. The electrochemical reactor employed potential value in such a way that the zinc reduction occurred under mass transport control. This potential was determined by hydrodynamic voltammetry using a borate/chloride solution as supporting electrolyte on stainless steel rotating disc electrode. The results indicate that mass transfer coefficient (Km) increases with increasing of flow rate (Q) where .The electrochemical reactor proved to be efficient in removing zinc and was abl

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Publication Date
Sun Jan 01 2017
Journal Name
Proceeding Of Second Thermal And Fluids Engineering Conference
Solidification Enhancement in Triplex-Tube Latent Thermal Energy Storage System Using a Combination of Nanoparticles and Fins
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Publication Date
Thu Jun 01 2023
Journal Name
Baghdad Science Journal
Simultaneous Determination of Piroxicam and Codeine Phosphate Hemihydrate in a Pharmaceutical Dosage Form Using Validated HPLC Method
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An easy, eclectic, precise high-Performance Liquid Chromatographic (HPLC) procedure was evolved and validated to estimate of Piroxicam and Codeine phosphate. Chromatographic demarcation was accomplished on a C18 column [Use BDS Hypersil C18, 5μ, 150 x 4.6 mm] using a mobile phase of methanol: phosphate buffer (60:40, v/v, pH=2.3), the flow rate was 1.1 mL/min, UV detection was at 214 nm. System Suitability tests (SSTs) are typically performed to assess the suitability and effectiveness of the entire chromatography system. The retention time for Piroxicam was found to be 3.95 minutes and 1.46 minutes for Codeine phosphate. The evolved method has been validated through precision, limit of quantitation, specificity,

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Publication Date
Fri Mar 01 2024
Journal Name
Baghdad Science Journal
A Comparison between Ericson's Formulae Results and Experimental Data Using New Formulae of Single Particle Level Density
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The partial level density PLD of pre-equilibrium reactions that are described by Ericson’s formula has been studied using different formulae of single particle level density . The parameter  was used from the equidistant spacing model (ESM) model and the non- equidistant spacing model (non-ESM) and another formula of  are derived from the relation between  and level density parameter . The formulae used to derive  are the Roher formula, Egidy formula, Yukawa formula, and Thomas –Fermi formula. The partial level density results that depend on  from the Thomas-Fermi formula show a good agreement with the experimental data.

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Publication Date
Mon Jul 10 2023
Journal Name
Sustainability
Solar-Induced Photocatalytic Degradation of Reactive Red and Turquoise Dyes Using a Titanium Oxide/Xanthan Gum Composite
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The present study explores the solar-induced photocatalytic degradation of reactive red (RR) and reactive turquoise (RT) dyes in a single system using TiO2 immobilized in xanthan gum (TiO2/XG), synthesized using the sol–gel dip-coating technique for direct precipitation. SEM-EDX, XRD, FTIR, and UV–Vis were used to assess the characteristics of the resulting catalyst. Moreover, the effects of different operating parameters, specifically pH, dye concentration, TiO2/XG concentration, H2O2 concentration, and contact time, were also investigated in a batch photocatalytic reactor. The immobilized TiO2/XG catalyst showed a slight adsorption degradation efficiency and then improved the RR and RT dye degradation activity (92.5 and 90.8%

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Publication Date
Sat Nov 01 2025
Journal Name
Journal Of Engineering
Improvement of Hot Mix Asphalt Resistance to Permanent Deformation at High Temperature Using Nanomaterial Modifiers: A Review
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The integration of nanomaterials in asphalt modification has emerged as a promising approach to enhance the performance of asphalt pavements, particularly under high-temperature conditions. Nanomaterials, due to their unique properties such as high surface area, exceptional mechanical strength, and thermal stability, offer significant improvements in the rheological properties, durability, and resistance to deformation of asphalt binders. This research reviewed the application of various nanomaterials, including nano silica, nano alumina, nano titanium, nano zinc, and carbon nanotubes in asphalt modification. The incorporation of these nanomaterials into asphalt mixtures has shown potential to increase the stiffness and high-tempera

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Publication Date
Fri Mar 01 2024
Journal Name
Baghdad Science Journal
Molecular detection of the ability of Biosynthesized Titanium dioxide nanoparticles to curing some genes of virulence factors of Entamoeba histolytica
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The present study included the microscopic and molecular identification of Entamoeba histolytica by using specific primers to detect four virulence factors possessed by Entamoeba histolytica. Virulence factors included Active Cysteine proteinase, Galactose/N-acetyl-D-galactose-lectin, Amoeba pore C and Phospholipase. Titanium dioxide nanoparticles (TiO2NPs) were synthesized from Pseudomonas aeruginosa which producing Pyocyanin pigment as a reducing agent to form it. After that we studied the ability ofTiO2NPs to inhibit virulence factors production and curing the genes responsible for encoding them by using four different dose 2 ,3, 4, 6 mg/Kg and administered by intraperitoneal injection

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Publication Date
Sat Sep 30 2017
Journal Name
Al-khwarizmi Engineering Journal
A Cognitive Hybrid Tuning Control Algorithm Design for Nonlinear Path-Tracking Controller for Wheeled Mobile Robot
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Abstract

This research presents a on-line cognitive tuning control algorithm for the nonlinear controller of path-tracking for dynamic wheeled mobile robot to stabilize and follow a continuous reference path with minimum tracking pose error. The goal of the proposed structure of a hybrid (Bees-PSO) algorithm is to find and tune the values of the control gains of the nonlinear (neural and back-stepping method) controllers as a simple on-line with fast tuning techniques in order to obtain the best torques actions of the wheels for the cart mobile robot from the proposed two controllers. Simulation results (Matlab Package 2012a) show that the nonlinear neural controller with hybrid Bees-PSO cognitive algorithm is m

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