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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
Fri Sep 05 2014
Journal Name
Engineering And Technology Journal
New Method to Increase the Ability of the Water for Dissolving Total Salts in Soil by Using the Magnetism
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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of The College Of Languages (jcl)
Al-Taa comparative studies among Semitic languages
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We have studied in this research litter (Taa) a morphological , sonic indicative and comparative study among four Semitic languages. They are Arabic , Hebrew, Syriac and Akkadian languages . We have divided the research into a number of pivots beginning with an entrance about the letter (Taa) in Semitic languages and the symbols which are used by these languages referring to . Then we have studied (Taa) from sonic side with letters phenomenon (b, g, k, p, t) the six in both Hebrew and Syriac languages . The letter (Taa) is formed one of them and the sonic change that is happening in articulation (Taa) according to sonic rules related to these letters in case of emphasis or in case of neglected (not emphasis). Then we have studied the pro

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
"RUF procedures forgetting the best subset linear regression model"
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The purpose behind building the linear regression model is to describe the real linear relation between any explanatory variable in the model and the dependent one, on the basis of the fact that the dependent variable is a linear function of the explanatory variables and one can use it for prediction and control. This purpose does not cometrue without getting significant, stable and reasonable estimatros for the parameters of the model, specifically regression-coefficients. The researcher found that "RUF" the criterian that he had suggested accurate and sufficient to accomplish that purpose when multicollinearity exists provided that the adequate model that satisfies the standard assumpitions of the error-term can be assigned. It

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Publication Date
Tue Mar 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Performance evaluation criteria"Applied Study in the General Company for the manufacture of glass and ceramics"
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Contemporary management is interested in the process of performance assessment  because of its significance in the field of planning and controlling the multiactiveties to attain its goals and uncovering digression of virtual performance after comparing it with the plan or equitable performance.

Digression is analyzed to enable management control centers of authority.

Assessment process significance is closely related by setting definite categories to evaluate the economic activity to know the ability to achieves aims.

This study concentrated on the most important categories that used to evaluate  company understudy with ather categories suggested to complete assessment process.

This study is in

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Publication Date
Wed Apr 01 2020
Journal Name
Iop Conference Series: Earth And Environmental Science
The Effect of Urban Form on Temperature for Hot Arid Zones. The Case Study of Baghdad, Iraq
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The research aims to determine optimal urban planning and design indicators of the urban clusters form in hot arid zones through studying of three urban areas in Baghdad, analyzing their urban indicators which include floor area ratio (FAR), urban clusters height, building density or land coverage, green areas, paved areas, shading ratio and how they affect urban temperature. The research reached the conclusion that air outdoor temperature on urban areas affected primarily by shadows casted on the ground, the effect of shaded area equals (5) times the effect of paved areas and (3.7) times the effect of green areas, this means that increasing urban clusters height in hot arid zones could minimize air outdoor temperature, building

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Publication Date
Sat Dec 30 2023
Journal Name
Journal Of Economics And Administrative Sciences
The Role of Digital Economy in Iraqi Economic Growth for The Period of 2010-2022 (Analytical Study)
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The research addresses the role of the digital economy in the growth of the Iraqi economy during the period from 2010 to 2022. The research is based on the hypothesis that the digital economy has become one of the primary growth drivers worldwide and has a close relationship with economic development. Therefore, the digital transformation in Iraq can accelerate bridging developmental gaps with other countries.

It has become evident that the Iraqi economy suffers from structural imbalances for various reasons, hindering economic growth. These reasons include political and economic factors, as well as the absence of a well-thought-out policy to promote the agricultural sector, which is considered one of the fundamental sectors capa

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Publication Date
Mon Mar 07 2022
Journal Name
Journal Of Educational And Psychological Researches
The Degree of Academic Leaders Practice at the University of Northern Border for Creative Leadership "Empirical Study"
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The study aimed to identify the degree of academic leaders practices at the University of Northern Border for creative leadership, which attribute to different variables (nature of work, employer, gender, years of experience in administrative work at the university). To achieve the goal of the study, the researcher used the descriptive approach survey. Therefore, the researcher used a questionnaire as a study tool, which consisted of (40) items that included dimensions (sensitivity to problems, initiative, originality, flexibility). The study sample consisted of (240) participants included (agents of colleges, and supporting deanships, and their employees) during the second semester of the academic year 1439/1440 AH. The results showed t

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Publication Date
Sun Dec 02 2012
Journal Name
Baghdad Science Journal
Morphological study of pollen-grains for the wild species of the genus Erysimum L. (Crucifereae) in Iraq
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Pollen grains morphology have been studied for the wild species of the genus Erysimum L. which belong to Crucifereae family in Iraq. These species are E. filifolium Boiss. et Hausskn., E. oleifolium J. Gay, E. repandum L., E. eginense Hausskn. ex Bornm., E. aucheranum J. Gay, E. cheiranthoides L., E. alpestre Ky. ex Boiss., E. kurdicum Boiss. et Hausskn., E. tenellum DC., E. strophades Boiss., E. gladiiferum Boiss. et Hausskn., E. nasturtioides Boiss. et Hausskn. The study was performe by using light microscope . The study reveal that there was only one type of pollen grain named Tricoplate in all studied species . The study also demonstrated that there were differences among pollen grains morphology . The species E. kurdicum , E. alpestre

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Publication Date
Tue Apr 30 2024
Journal Name
International Review Of Electrical Engineering (iree)
Enhancing Efficiency in Distribution Power Networks by Power Factor Controlling of Renewable Energy Generators: a Case Study of Iraqi Wasit Network
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Integrating Renewable Energy (RE) into Distribution Power Networks (DPNs) is a choice for efficient and sustainable electricity. Controlling the power factor of these sources is one of the techniques employed to manage the power loss of the grid. Capacitor banks have been employed to control phantom power, improving voltage and reducing power losses for several decades. The voltage sag and the significant power losses in the Iraqi DPN make it good evidence to be a case study proving the efficiency enhancement by adjusting the RE power factor. Therefore, this paper studies a part of the Iraqi network in a windy and sunny region, the Badra-Zurbatya-11 kV feeder, in the Wasit governorate. A substation of hybrid RE sources is connected to this

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Publication Date
Thu Feb 01 2024
Journal Name
Journal Of Engineering
Assessment of Bearing Capacity and Settlement Characteristics of Organic Soil Reinforced by Dune Sand and Sodium Silicate Columns: A Numerical Study
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Organic soil is problematic soils in geotechnical engineering due to its properties, as it is characterized by high compressibility and low bearing capacity. Therefore, several geotechnical techniques tried to stabilize and improve this soil type. In this study, sodium silicate was used to stabilize sand dune columns. The best sodium silicate concentration (9%) was used, and the stabilized sand dune columns were cured for seven days. The results for this soil were extracted using a numerical analysis program (Plaxis 3D, 2020).In the case of studying the effect of (L/D) (where ‘’L” and ‘’D’’ length and diameter of sand dune columns) of a single column of sand dunes stabilized with sodium silicate with a diff

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