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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 Aug 03 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of the forensic accounting philosophy in the transparency and quality of financial statements: : An applied study on a sample of workers at the Trade bank of Iraq and the Gulf Commercial Bank in Babylon
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This research aims to identify the role that forensic accounting plays on the transparency and quality of the financial statements in trade bank of Iraq and the Gulf Commercial Bank in Babylon. This research came to address the problem that most financial institutions suffer from, which is represented by the lack of transparency and the quality of the financial statements issued in a manner. Annual also the manipulation and fraud in the financial data, which causes a big gap between that institutions and organizational stakeholders. According to the implementation of the research hypothesis and the objectives of the research, a questionnaire was prepared consisting of three axes, the first axis dealing with the demographic distri

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Publication Date
Thu Oct 31 2013
Journal Name
Al-khwarizmi Engineering Journal
Simulation of a Wet Sulfuric Acid Process (WSA) for Utilization of Acid Gas Separated from Omani Natural Gas
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In this study, a proposed process for the utilization of hydrogen sulphide separated with other gases from omani natural gas for the production of sulphuric acid by wet sulphuric acid process (WSA) was studied. The processwas simulated at an acid gas feed flow of   5000 m3/hr using Aspen ONE- V7.1-HYSYS software. A sensitivity analysis was conducted to determine the optimum conditions for the operation of plant. This included primarily the threepacked bed reactors connected in series for the production of sulphur trioxidewhich represented the bottleneck of the process. The optimum feed temperature  and catalyst bed volume for each reactor were estimated and then used in the simulation of the whole process for tw

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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
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Physics
Study the effect of Iraqi weather parameter in FSO communication using different wavelength (650, 532) nm
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Light has already becomes a popular means of communication, and the high-bandwidth data into free space without the use of wires. A great idea took us to design a new system for transmitting sound through free space at (650, 532) nm wavelengths using reflective mirrors under different atmospheric conditions. The study showed us the effect of various weather factors (temperature, wind speed and humidity) on these wavelengths for different distances. As well as studying the attenuation caused by long-distance laser and beam divergence, A reflective dish was used to focus the spot of the laser beam on the photocell. Results were discussed under the effect of these factors and the attenuation resulting from the beam divergence. Thus, the sys

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The impact of monetary policy variables inflation in Algeria: standard study using self regression time gaps
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                In the past years, the Algerian Economy has witnessed various monetary developments characterized by different monetary and banking reforms aimed by monetary authorities to achieve monetary stability and driving overall growth. It should be noted that there is evidence to initiate fundamental changes on the basis of which new monetary, financing and banking policy mechanisms must be formulated in Algeria by enhancing the pursuit of reforming the monetary system, in order to improve monetary and economic indicators.

                The study a

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Publication Date
Sun Oct 19 2025
Journal Name
Lecture Notes In Networks And Systems
The Impact of Black Marketing on Purchasing Decisions: An Exploratory Study Using AI-Driven Analytical Tools
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Publication Date
Fri Aug 30 2024
Journal Name
Iraqi Journal Of Science
The Dissipation of the Kinetic Energy for 2D Bounded Flow by Using Moment-Based Boundary Conditions with Burnett Order Stress for LBM
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     In this article, the lattice Boltzmann method with two relaxation time  (TRT)  for the  D2Q9 model is used to investigate numerical results for 2D flow. The problem is performed to show the dissipation of the kinetic energy rate and its relationship with the enstrophy growth for 2D dipole wall collision. The investigation is carried out for normal collision and oblique incidents at an angle of . We prove the accuracy of moment -based boundary conditions with slip and Navier-Maxwell slip conditions to simulate this flow. These conditions are under the effect of Burnett-order stress conditions that are consistent with the discrete Boltzmann equation. Stable results are found by using this kind of boundary condition where d

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Publication Date
Sun Oct 19 2025
Journal Name
Lecture Notes In Networks And Systems
The Effect of Skill and Physical Exercises Using Smart Virtual Reality for Volleyball Players
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Publication Date
Sat May 09 2015
Journal Name
International Journal Of Innovations In Scientific Engineering
USING ARTIFICIAL NEURAL NETWORK TECHNIQUE FOR THE ESTIMATION OF CD CONCENTRATION IN CONTAMINATED SOILS
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The aim of this paper is to design artificial neural network as an alternative accurate tool to estimate concentration of Cadmium in contaminated soils for any depth and time. First, fifty soil samples were harvested from a phytoremediated contaminated site located in Qanat Aljaeesh in Baghdad city in Iraq. Second, a series of measurements were performed on the soil samples. The inputs are the soil depth, the time, and the soil parameters but the output is the concentration of Cu in the soil for depth x and time t. Third, design an ANN and its performance was evaluated using a test data set and then applied to estimate the concentration of Cadmium. The performance of the ANN technique was compared with the traditional laboratory inspecting

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Publication Date
Sun Oct 19 2025
Journal Name
Lecture Notes In Networks And Systems
The Effect of Skill and Physical Exercises Using Smart Virtual Reality for Volleyball Players
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