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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
Thu Feb 28 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Role of Job Enrichment in Building Differentiation Strategy Service: Analytical Exploratory Study of the Views of a Sample of the General Managers and Heads of Departments and Officials of the People in the General Establishment of Civil Aviation
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According to the importance of the subject of research, and the importance of the surveyed organization as a dynamic sector of the country in general , The research attempts to suggest to service organizations in general reconsidering the currently adopted mechanisms in the redesign of its functions , and in the services provided industry . The data was collected from (98) Director Mangers , head of department and head of division . The research tool is the questionnaire , which included (50) items . The results show Significant Effect & Correlation relationship between the two variables due to their dimensions . These lead to he application of job enrichment technology will increase the organization's ability to possess efficient hu

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Comparison Between Ordinary Methods (LS,IV) and Robust Methods (2SWLS,LTS,RA) to estimate the Parameters of ARX(1,1,1) Model for Electric Loads
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Abstract:

The models of time series often suffer from the problem of the existence of outliers ​​that accompany the data collection process for many reasons, their existence may have a significant impact on the estimation of the parameters of the studied model. Access to highly efficient estimators  is one of the most important stages of statistical analysis, And it is therefore important to choose the appropriate methods to obtain good  estimators. The aim of this research is to compare the ordinary estimators and the robust estimators of the estimation of the parameters of

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Publication Date
Thu May 16 2019
Journal Name
Al-khwarizmi Engineering Journal
Study of Transverse and Longitudinal Crack Propagation in Human Bone Using the Finite Element Method with MATLAB
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A finite element is a study that is capable of predicting crack initiation and simulating crack propagation of human bone. The material model is implemented in MATLAB finite element package, which allows extension to any geometry and any load configuration. The fracture mechanics parameters for transverse and longitudinal crack propagation in human bone are analyzed. A fracture toughness as well as stress and strain contour are generated and thoroughly evaluated. Discussion is given on how this knowledge needs to be extended to allow prediction of whole bone fracture from external loading to aid the design of protective systems.

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Publication Date
Tue Feb 28 2023
Journal Name
Egyptian Journal Of Chemistry
Application of UV-A light Operating Photoreactor for Green Degradation of Direct Blue 15 through the Photo-Fenton-like process: Effects and Box-Behnken Optimization
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Publication Date
Tue Nov 01 2022
Journal Name
Al-adab Journal
A Pragmatic Analysis of Implicatures in Covid-19 Coronavirus English Jokes: A Neo-Gricean Approach
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Publication Date
Thu Jun 30 2016
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
CFD Simulation of Air Flow Patterns in a Spray Dryer Fitted With a Rotary Disk
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The air flow pattern in a co-current pilot plant spray dryer fitted with a rotary disk atomizer was determined experimentally and modelled numerically using Computational Fluid Dynamics (CFD) (ANSYS Fluent ) software. The CFD simulation used a three dimensions system, Reynolds-Average Navier-Stokes equations (RANS), closed via the RNG k −ε turbulence model. Measurements were carried out at a rotation of the atomizer (3000 rpm) and when there is no rotation using a drying air at 25 oC and  air velocity at the inlet of  5 m/s without swirl. The air flow pattern was predicted experimentally using cotton tufts and digital anemometer. The CFD simulation predicted a downward central flowing air core surrounded by a slow

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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of The Faculty Of Languages
A Psychological Reading of The Problem of the Black in John Steinbeck’s Of Mice and Men
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Publication Date
Thu Jan 02 2020
Journal Name
Journal Of The College Of Languages (jcl)
A Psychological Reading of The Problem of the Black in John Steinbeck’s Of (Mice and Men)
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The present paper applies Fanon Psychological reading of the problem of the Black introduced in his book Black Skin White Mask to Crooks, The black Character in John Steinbeck’s  Of Mice and Men. The analysis of this character infers three essential points regarding the artistic achievement of the author. First, he uses a fictional character that offers a psychological interpretation of the black problem of alienation and loneliness in a way that does not disgrace the black. Second, he applies Fanon’s way of showing the various attitudes that the black adopts in contact with the white society. Third, he affirms that the black inferiority complex comes as a result of double proc

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Publication Date
Wed Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
Attitude The King Ghazi a Problem the Border with Kuwait 1933-1939
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King Ghazi (1933-1939) was of the Arabic characters that characterized national and
patriotic spirit and that faced the British policy in all its aspects.
King Ghazi distinguished as of Arab nationalist tendencies and called for the
liberalization of Arab lands which were under the rule of the Ottoman Empire. He called for
reunification under the one Arab country, Hence came the King invitations to liberate Kuwait
from the British protectorate and consolidated with Iraq.
King Ghazi established a private radio station in the royal palace (AL zzaahoor) palace
and provided special programs to return of Kuwait to Iraq, this radio station was The
prominent role in the revitalization of the Kuwaiti National Movement, an

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Publication Date
Mon Aug 16 2021
Journal Name
TÜrkÇe SÖzlÜkte Tdk Yer Alan ArapÇa Kelİmeler Üzerİne Bİr Anlam Bİlİmİ İncelemesİ
A SEMANTICS REVIEW ON THE ARABIC WORDS IN THE TURKISH DICTIONARY (TDK)
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