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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
Wed Sep 01 2010
Journal Name
Al-khwarizmi Engineering Journal
Extraction of Monocyclic Aromatic Hydrocarbons From Petroleum Products Using Sulfolane as Industrial Solvent
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            Liquid – liquid equilibria data were measured at 293.15 K for the pseudo ternary system (sulfolane + alkanol) + octane + toluene. It is observed that the selectivity of pure sulfolane increases with cosolvent methanol but decreases with increasing the chain length of hydrocarbon in 1-alkanol. The nonrandom two liquid (NRTL) model, UNIQUAC model and UNIFAC model were used to correlate the experimental data and to predict the phase composition of the systems studied. The calculation based on NRTL model gave a good representation of the experimental tie-line data for all systems studied. The agreement between the correlated and the experimental results was very good

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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Engineering
Decolorizing of Malachite Green Dye by Adsorption Using Corn Leaves as Adsorbent Material
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This paper presents the ability to use cheap adsorbent (corn leaf) for the removal of Malachite Green (MG) dye from its aqueous solution. A batch mode was used to study several factors, dye concentration (50-150) ppm, adsorbent dosage (0.5-2.5) g/L, contact time (1-4) day, pH (2-10), and temperature (30-60)   The results indicated that the removal efficiency increases with the increase of adsorbent dosage and contact time, while inversely proportional to the increase in pH and temperature. An SEM device characterized the adsorbent corn leaves. The adsorption's resulting data were in agreement with Freundlich isotherm according to the regression analysis, and the kinetics data followed pseudo-first-or

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Publication Date
Mon Mar 02 2026
Journal Name
Sciences Journal Of Physical Education
Leadership patterns for university student activities managers according to the Blake and Moton model (The managerial Grid)
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The researcher is one of the workers in university sports student activities, as he noticed that there is a diversity in the use of leadership patterns among managers of student activities in Iraqi universities between one director and another, which leads to the impact of these leadership styles on performance, positive or negative, in the level of human relations and the achievement of results. The researcher adopted the descriptive method in the survey method with relational relationships. The research sample consisted of (184) sports coaches who represent (27) universities and governmental and private colleges. To achieve the research objectives, the researcher used the Statistical Package for Social Sciences (Spss). To extract.statisti

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Publication Date
Thu Nov 03 2022
Journal Name
Frontiers In Applied Mathematics And Statistics
Prey fear of a specialist predator in a tri-trophic food web can eliminate the superpredator
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We propose an intraguild predation ecological system consisting of a tri-trophic food web with a fear response for the basal prey and a Lotka–Volterra functional response for predation by both a specialist predator (intraguild prey) and a generalist predator (intraguild predator), which we call the superpredator. We prove the positivity, existence, uniqueness, and boundedness of solutions, determine all equilibrium points, prove global stability, determine local bifurcations, and illustrate our results with numerical simulations. An unexpected outcome of the prey's fear of its specialist predator is the potential eradication of the superpredator.

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Publication Date
Mon Oct 20 2025
Journal Name
Научный форум
Strategies of cultural adaptation and linguistic russification in the muravyov-kistyakovsky translation of 'the fellowship of the ring' (1982): a comprehensive study of fantasy text domestication
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This study examines strategies of cultural domestication in Muravyov and Kistyakovsky’s Russian translation of (The Fellowship of the Ring). It documents transformations of character names, toponyms, dialogues, and cultural references, highlighting systematic Russification and the infusion of Soviet political commentary that reshape the text into cultural rewriting.

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Publication Date
Thu Jan 23 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
EFFECT OF DECISION OF INCREASING THE MINIMUM LIMIT OF THE CAPITAL IN THE IRAQI PRIVATE BANKING ACTIVITY: APPLIED STUDY IN A SAMPLE OF PRIVATE IRAQI BANKS
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This research aims to show the sight at the importance of the private banking sector in Iraq and its role in financing of the investment projects , of the ability of Central Bank's decision to increase the minimum limit of capital for private banks to provide support to the economic activity and the development in Iraq. In addition to illustrate the importance of the capital increase, with a, and taking into notice the most important determinants that can stand in front of these banks in the beginning of the decision implementation, which in turn can lead to the most important proceedings that can contribute in the support of banks to implementation the decision.  Also, the research has highlighted the most important ways through wh

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Publication Date
Tue Jun 01 2021
Journal Name
Baghdad Science Journal
Influence of Varying Temperature and Concentration on Magnetohydrodynamics Peristaltic Transport for Jeffrey Fluid with a Nanoparticles Phenomenon through a Rectangular Porous Duct
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A mathematical model constructed to study the combined effects of the concentration and the thermodiffusion on the nanoparticles of a Jeffrey fluid with a magnetic field effect the process of containing waves in a three-dimensional rectangular porous medium canal. Using the HPM to solve the nonlinear and coupled partial differential equations. Numerical results were obtained for temperature distribution, nanoparticles concentration, velocity, pressure rise, pressure gradient, friction force and stream function. Through the graphs, it was found that the velocity of fluid rises with the increase of a mean rate of volume flow and a magnetic parameter, while the velocity goes down with the increasing a Darcy number and lateral walls. Also, t

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Publication Date
Sun Sep 01 2024
Journal Name
Results In Engineering
Implementation of a control and monitoring system for a cathodic protection cell to mitigate localized corrosion in fixed and mobile steel structures
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Publication Date
Sun Sep 01 2024
Journal Name
Results In Engineering
Implementation of a control and monitoring system for a cathodic protection cell to mitigate localized corrosion in fixed and mobile steel structures
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The current study introduces a novel technique to handle electrochemical localized corrosion in certain limited regions rather than applying comprehensive cathodic protection (CP) treatment. An impressed current cathodic protection cell (ICCPC) was fabricated and firmly installed on the middle of a steel structure surface to deter localized corrosion in fixed or mobile steel structures. The designed ICCPC comprises three essential parts: an anode, a cathode, and an artificial electrolyte. The latter was developed to mimic the function of the natural electrolyte in CP. A proportional-integrated-derivative (PID) controller was designed to stabilize this potential below the ICCPC at a cathodic potential of −850 mV, which is crucial for prote

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Publication Date
Thu Jun 08 2023
Journal Name
Iraqi Journal Of Laser
PDF Lab-On-a-Chip an integrated microfluidic device sensitive low-Cost, and Rapid with a syringe pump for Analysis of Ibuprofen
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Abstract: Microfluidic devices present unique advantages for the development of efficient drug assay and screening. The microfluidic platforms might offer a more rapid and cost-effective alternative. Fluids are confined in devices that have a significant dimension on the micrometer scale. Due to this extreme confinement, the volumes used for drug assays are tiny (milliliters to femtoliters).

 In this research, a microfluidic chip consists of micro-channels carved on substrate materials built by using Acrylic (Polymethyl Methacrylate, PMMA) chip was designed using a Carbon Dioxide (CO2) laser machine. The CO2 parameters have influence on the width, depth, roughness of the chip. In order to have regular

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