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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 Sep 09 2014
Journal Name
Iosr Journal Of Mathematics (iosr-jm)
An Efficient Shrinkage Estimator for the Parameters of Simple Linear Regression Model
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Studying the Behavior of Asphalt Stabilized Gepseous Soil for Earth Embankment Model
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The study presents the test results of stabilizing gypseous soil embankment obtained from
Al- Faluja university Campus at Al-Ramady province. The laboratory investigation was divided
into three phases, The physical and chemical properties, the optimum liquid asphalt (emulsion)
requirements (which are manufactured in Iraq) were determined by using one dimensional
unconfined compression strength test.in the first phase , The optimum fluid content was 11%
(6% of emulsion with 5% water content).. At phase two, the effect of Aeration technique was
investigated using both direct shear and permeability test. At phase three for the case of static
load , the pure soil embankment model under dry test condition was investigated

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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 PhÓ“nomen in vier ausgewÓ“hlten 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
Thu May 06 2010
Journal Name
Dirasat, Pure Sciences
A Study of the Effects of the Solar Cycle 22, on the Critical Frequencies of F1 Layer over Baghdad
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This paper aims to study the effects of the long term solar activity on the critical frequencies of ionospheric F1 layer over Baghdad city, during the solar cycle 22, within (1988- 1995). It is found that the critical frequency of this layer is closely related to the sunspots number during the years of the solar cycle 22, at a middle latitude region of the world. The study discussed the effect of sunspot numbers and solar events on the electron densities of F1 layer, which is the most important ionospheric parameter.

Publication Date
Sat Aug 01 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
Building and legalizing a test for evaluating the tactical learning of the footwork for the foil fencer in the fencing game
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AA wahid, journal mustansiriyah of sports science, 2023

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Publication Date
Fri Nov 01 2019
Journal Name
Civil Engineering Journal
Time-Cost-Quality Trade-off Model for Optimal Pile Type Selection Using Discrete Particle Swarm Optimization Algorithm
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The cost of pile foundations is part of the super structure cost, and it became necessary to reduce this cost by studying the pile types then decision-making in the selection of the optimal pile type in terms of cost and time of production and quality .So The main objective of this study is to solve the time–cost–quality trade-off (TCQT) problem by finding an optimal pile type with the target of "minimizing" cost and time while "maximizing" quality. There are many types In the world of piles but  in this paper, the researcher proposed five pile types, one of them is not a traditional, and   developed a model for the problem and then employed particle swarm optimization (PSO) algorithm, as one of evolutionary algorithms with t

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Publication Date
Sun Aug 13 2023
Journal Name
Arpn Journal Of Engineering And Applied Sciences
A NEW APPROACH FOR MODELLING THE VIBRATION OF BEAMS UNDER MOVING LOAD EFFECT
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In this paper, a new equivalent lumped parameter model is proposed for describing the vibration of beams under the moving load effect. Also, an analytical formula for calculating such vibration for low-speed loads is presented. Furthermore, a MATLAB/Simulink model is introduced to give a simple and accurate solution that can be used to design beams subjected to any moving loads, i.e., loads of any magnitude and speed. In general, the proposed Simulink model can be used much easier than the alternative FEM software, which is usually used in designing such beams. The obtained results from the analytical formula and the proposed Simulink model were compared with those obtained from Ansys R19.0, and very good agreement has been shown. I

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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
Thu Jul 16 2020
Journal Name
Diyala Agricultural Sciences Journal
A FINANCIAL ANALYSIS OF AGRICULTURAL COMPANIES IN IRAQ FOR THE PERIOD (2005-2016)
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Agricultural companies could push investment forward and help in production base variation and developing production techniques. They also play a significant role in organizing and providing requirements of market economy. This work aimed at studying economic efficiency of the six agricultural companies that are registered at Iraqi stock market for the period 2005-2016. Capital of these companies was between (300 million-7.5 billion IQD). Several financial analysis indicators were applied such as activity percentages. Average of capital circulation was 0.91 for private company of agricultural production، and lowest share was for Iraqi company for producing and marketing field crops. Assets average circulation was highest for the pr

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