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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
Mon Jan 01 2024
Journal Name
Recent Research On Geotechnical Engineering, Remote Sensing, Geophysics And Earthquake Seismology
Evaluating the Accuracy of iPhone Lidar Sensor for Building Façades Conservation
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Publication Date
Wed May 29 2019
Journal Name
Journal Of Legal Sciences
The extent of responsibility - the seller of Alcohol or the provider – the civil towards the drug addicts and their victims "A comparative study"
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There are many harmful acts that occur from drunkards in this case, especially those resulting from car accidents. The world is witnessing dozens or even hundreds of car accidents due to alcohol consumption. These accidents often result in serious injuries that could lead to the death of the drunk driver and those in the car As well as other persons present in the other vehicles with which the incident occurred or pedestrians on the street, as well as damage to private or public property, and if the order of return of the affected persons on the pretext of civil liability (tort) is made as a direct cause of the harmful act, Is entitled Do they like this refer to the liquor seller or their provider as the culprit? Or are they not related to

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Publication Date
Mon Nov 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Building a model to reduce the cost of hajj in the Iraqi Authority for Hajj and Umrah
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The research is summarized in the construction of a mathematical model using the most common methods in the science of Operations Research, which are the models of transportation and linear programming to find the best solution to the problem of the high cost of hajj in Iraq, and this is done by reaching the optimum number of pilgrims traveling through both land ports and the number Ideal for passengers traveling through airports by Iraqi Airways, instead of relying on the personal experience of the decision-maker in Hajj and Umrah Authority by identifying the best port for pilgrim's travel, which can tolerate right or wrong, has been based on scientific methods of Operations Research, the researcher built two mathematical models

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Publication Date
Thu Sep 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
360 degree reverse feedback / comparative analytical study for a sample of managers and heads of departments in the Central Electricity DepartmentAnd the General Directorate of Water and Sewage
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يسعى البحث إلى الاهتمام بإحدى الوظائف المهمة في إدارة الموارد البشرية وهي تقويم الأداء التي تواجه مجموعة من الانتقادات والآراء السلبية، اذ ظهر في الأّونة الأخيرة أنموذج جديد يمكن إن يتجاوز تلك السلبيات وهو أنموذج التغذية العكسية المتعدد المصادر درجة .وقد حاول الباحثان توظيف هذا المفهوم في اثنتين من المنظمات العامة العراقية هما (دائرة كهرباء الوسط) التابعة لوزارة الكهرباء
و (دائرة الماء والمجاري) ال

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Publication Date
Thu Oct 12 2017
Journal Name
Iraqi Journal Of Laser
A Comparative Evaluation of Post-Operative Pain and Function after Gingival Depigmentation Using 940 Nm Diode Laser And Conventional Bur Method: 6 Months Study
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The aim of the study was to evaluate the efficacy of diode laser (λ=940 nm) in the management of gingival hyperpigmentation compared to the conventional bur method. Materials and methods: Eighteen patients with gingival hyperpigmentation were selected for the study with an age between 12-37 years old. The site of treatment was the upper gingiva using diode laser for the right half and the conventional method for the left half. All patients were re-evaluated after the following intervals: 3 days, 7 days, 1 month and 6 months post-operation. Pain and functions were re-evaluated in each visit for a period of 1 day, 3 days and 1 week post-operation. Laser parameters included 1.5 W in continuous mode with an initiated tip (400 μm) placed in

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Extent of the Practice of Iraqi Banks to Manage Profits Using the (LLp it) Model and Its Reflection on the Tax Base, A Case Study of A Sample of Iraqi Private Banks Listed in The Iraqi Stock Exchange
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The research aims to identify the extent to which Iraqi private banks practice profit management motivated by reducing the taxable base by increasing the provision for loan losses by relying on the LLP it model, which consists of a main independent variable (net profit before tax) and independent sub-variables (bank size, total debts to total equity, loans granted to total obligations) under the name of the variables governing the banking business. (Colmgrove-Smirnov) was used to test the normal distribution of data for all banks during the period 2017-2020, and then find the correlation between the main independent variable sub and the dependent variable by means of the correlation coefficient person, and then using the multiple

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Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Semiotics of Musical Sign in Iraqi Pantomime Show (Ahriman) as a Model: علي عدي صاحب-شيماء حسين طاهر
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The musical sign was associated with the first appearances of acting that are based on human gestures and expressive and silent movements, and they contributed in accentuating and clarifying these gestures and explain their meanings and indications, and they remained with them until these gestures turned into artistic theatrical shows so that the musical sign would have many functions and constitute the main pillars for this kind of show.
The musical sign is a language not much different than the human language in the semiotic analysis. There has been an increased interest in it and its use in the mime shows by the graduates who realized its necessity and significance in the pantomime show intellectually, artistically and aesthetical

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Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
A Study of the electronic structure of CdS Nanocrystals using density functional theory
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Density Functional Theory at the generalized-gradient approximation level coupled with large unit cell method is used to simulate the electronic structure of (II-VI) zinc-blende cadmium sulfide nanocrystals that have dimensions 2-2.5 nm. The calculated properties include lattice constant, conduction and valence bands width, energy of the highest occupied orbital, energy of the lowest unoccupied orbital, energy gap, density of states etc. Results show that lattice constant and energy gap converge to definite values. However, highest occupied orbital, lowest unoccupied orbital fluctuates indefinitely depending on the shape of the nanocrystal.

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Educational And Psychological Researches
Teaching skills for Public and Private Schools’ Teachers: comparative study : Teaching skills for Public and Private Schools’ Teachers: comparative study
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Abstract:

The great expansion of teaching skills requires finding ways and methods to help teachers acquire experiences of all kinds. The researcher found in the subject of the teaching skills for teachers in public and private schools a fertile field for conducting a study that enables the measurement of these skills. Thus, the study aims to identify the skills of teaching lessons for teachers, the difference in teaching lesson skills for teachers according to the years of service, the differences in teaching lesson skills for teachers according to the specialized teachers and non-specialized teachers, the differences in teaching lesson skills for teachers according to the public and private school. The

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Publication Date
Mon Jun 01 2020
Journal Name
Iraqi Journal Of Physics
Theoretical Model for Spectroscopic Study of Cu+2, Co+2, and Fe+3 Dissolved in Ethanol with A Different Concentrations
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The absorption spectrum for three types of metal ions in different concentrations has been studying experimentally and theoretically. The examination model is by Gaius model in order to find the best fitting curve and the equation controlled with this behavior. The three metal ions are (Copper chloride Cu+2, Iron chloride Fe+3, and Cobalt chloride Co+2) with different concentrations (10-4, 10-5, 10-6, 10-7) gm/m3. The spectroscopic study included UV-visible and fluorescence spectrum for all different concentrations sample. The results refer to several peaks that appear from the absorption spectrum in the high concentration of all metal ions solution.

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