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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 Mar 25 2015
Journal Name
Comptes Rendus Chimie
A novel method for the synthesis of biodiesel from soybean oil and urea
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The increasing demand for energy has encouraged the development of renewable resources and environmentally benign fuel such as biodiesel. In this study, ethyl fatty esters (EFEs), a major component of biodiesel fuel, were synthesized from soybean oil using sodium ethoxide as a catalyst. By-products were glycerol and difatty acyl urea (DFAU), which has biological characteristics, as antibiotics and antifungal medications. Both EFEs and DFAU have been characterized using Fourier transform infrared (FTIR) spectroscopy, and 1H nuclear magnetic resonance (NMR) technique. The optimum conditions were studied as a function of reaction time, reactant molar ratios, catalyst percentage and the effect of organic solvents. The conversion ratio of soybea

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Publication Date
Tue Oct 13 2015
Journal Name
Plos Medicine
P2RX7 Purinoceptor: A Therapeutic Target for Ameliorating the Symptoms of Duchenne Muscular Dystrophy
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Publication Date
Thu Jun 30 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Adopting opportunity cost as a tool to increase tax revenue: Applied research in the General Tax Authority - Companies Division
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This research seeks to try to address one of the important issues in society that prevents the state from achieving its social, economic, political and financial goals, represented by the low tax proceeds, through which it can achieve those goals. What is reflected on the tax proceeds, knowing that the General Tax Authority does not take into account the issue of analyzing the opportunity cost of corporate capital as one of the profit indicators when setting the annual controls, which leads to a decrease in the tax proceeds, and therefore the research objective will be to shed light on the importance of adopting the concept of analysis The opportunity cost by the General Tax Authority to achieve a tax proceeds commensurate with t

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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of The College Of Languages (jcl)
The passive As a grammatical phenomenon in four selected textbooks: Das Passiv Als grammatisches Phӓnomen in vier ausgewӓhlten Lehrwerken
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The research work is "The passive voice as a grammatical phenomenon in four selected textbooks". The research deals with the grammatical phenomenon passive in German. The research consists of two parts, the theoretical and the empirical part. The present research work is divided into 3 sections:

The first section includes the definition of passive, passive types, process passive, state passive, passive with modal verbs, and other types of passive. The second section provides illustrations of the four selected textbooks. The third chapter presents the passive voice in textbooks, namely German language teaching for foreigners by Dora Schulz and Heinz Griesbach, Delfin von Aufderstrasse H. and others, Em von Balme, M. and others and

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Publication Date
Mon Jan 01 2018
Journal Name
Al-dhad Book Store And Publishing
Calculus part 1
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This book includes three main chapters: 1. Functions & Their Derivatives. 2. Minimum, Maximum and Inflection points. 3. Partial Derivative. In addition to many examples and exercises for the purpose of acquiring the student's ability to think correctly in solving mathematical questions.

Publication Date
Fri May 16 2025
Journal Name
Tikrit Journal Of Engineering Sciences
Comparative Study of Activated Carbon and Silver Nanoparticle-Loaded Activated Carbon Derived from Tea Waste for Removal of Tetracycline from Aqueous Solution
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The present work elucidates the utilization of activated carbon (AC) and activated carbon loaded with silver nanoparticles (AgNPs-AC) to remove tetracycline (TC) from synthetically polluted water. The activated carbon was prepared from tea residue and loaded with silver nanoparticles. Scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and Brunauer-Emmett-Teller (BET) were used to characterize the activated carbon (AC) and silver nanoparticles-loaded activated carbon (AgNPs-AC). The impact of various parameters on the adsorption effectiveness of TC was examined. These variables were the initial adsorbate concentration (Co), solution acidity (pH), adsorption time (t), and dosag

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Publication Date
Mon Jun 01 2015
Journal Name
Iraqi Journal Of Science
Simulation of Solar Coronal Magnetic Field Using Potential Field Model
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In this paper, 3D simulation of the global coronal magnetic field, which use observed line of sight component of the photosphere magnetic field from (MDI/SOHO) was carried out using potential field model. The obtained results, improved the theoretical models of the coronal magnetic field, which represent a suitable lower boundary conditions (Bx, By, Bz) at the base of the linear force-free and nonlinear force free models, provides a less computationally expensive method than other models. Generally, very high speed computer and special configuration is needed to solve such problem as well as the problem of viewing the streamline of the magnetic field. For high accuracy special mathematical treatment was adopted to solve the computation comp

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Publication Date
Fri Aug 23 2013
Journal Name
International Journal Of Computer Applications
Lossless Compression of Medical Images using Multiresolution Polynomial Approximation Model
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In this paper, a simple fast lossless image compression method is introduced for compressing medical images, it is based on integrates multiresolution coding along with polynomial approximation of linear based to decompose image signal followed by efficient coding. The test results indicate that the suggested method can lead to promising performance due to flexibility in overcoming the limitations or restrictions of the model order length and extra overhead information required compared to traditional predictive coding techniques.

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Publication Date
Sun Feb 05 2017
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
STUDY THE OPTIMUM CONDITIONS FOR THE REMOVAL OF HEAVY METAL ELEMENTS FROM AQUEOUS SOLUTIONS USING CONTAMINATED BACTERIA Bacillus subtilis LOCALLY ISOLATED: STUDY THE OPTIMUM CONDITIONS FOR THE REMOVAL OF HEAVY METAL ELEMENTS FROM AQUEOUS SOLUTIONS USING CONTAMINATED BACTERIA Bacillus subtilis LOCALLY ISOLATED
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We studied the effect of certain environmental conditions for removing heavy metal elements from contaminated aqueous solutions (Cd, Cu, Pb, Fe, Zn, Ni, Cr) using the bacterium Bacillus subtilis to appoint the optimal conditions for removal ,The best optimum temperature range for two isolate was 30-35○C while the hydrogen number for the maximum mineral removal range was 6-7. The best primary mineral removal was 100 mg/L, while the maximum removal for all minerals was obtained after 6 hrs of Cu element time and the maximum removal efficiency was obtained after 24 hrs of Cu element. The results have proved that the best aeration for maximum removal was obtained at rotation speed of 150 rpm/minute. Inoculums of 5ml/100ml which contained 1

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Publication Date
Tue Jan 01 2019
Journal Name
Australian Journal Of Mathematical Analysis And Applications
Formulation of approximate mathematical model for incoming water to some dams on Tigris and Euphrates Rivers using spline function
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n this paper, we formulate three mathematical models using spline functions, such as linear, quadratic and cubic functions to approximate the mathematical model for incoming water to some dams. We will implement this model on dams of both rivers; dams on the Tigris are Mosul and Amara while dams on the Euphrates are Hadetha and Al-Hindya.

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