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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
Sun May 28 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
On-Line Navigational Problem of a Mobile Robot Using Genetic Algorithm
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Publication Date
Thu Oct 31 2019
Journal Name
Al-kindy College Medical Journal
Using Zinc in Management of Subfertile Male Patients: a Clinical Trial
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Background: The use of minerals in treatment of different diseases is as old as man himself. zinc is the most famous trace mineral related to male sexual function. Oligoasthenozoospermic subfertile patients were treated with zinc sulphate for three months.

Objectives: Aim of the research is to investigate the role of Zinc and if it affects the abnormalities of some semen parameters and to study the possible role of pharmaceutical preperations of zinc in amelioration of male subfertility as well as to assess the ability of Zinc to induce changes in the serum and semen zinc levels in addition to the levels of reproductive hormones (FSH and Testosterone).

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Publication Date
Thu Jul 01 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A proposed encryption technique of different texts using circular link lists
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Publication Date
Wed Aug 12 2020
Journal Name
International Journal On Advanced Science, Engineering And Information Technology
Developing of a 3D Printer to Produce Parts Using Powder Metal
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Publication Date
Thu Mar 09 2023
Journal Name
Coatings
Nondestructive Evaluation of Fiber-Reinforced Polymer Using Microwave Techniques: A Review
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Carbon-fiber-reinforced polymer (CFRP) is widely acknowledged as a leading advanced material structure, offering superior properties compared to traditional materials, and has found diverse applications in several industrial sectors, such as that of automobiles, aircrafts, and power plants. However, the production of CFRP composites is prone to fabrication problems, leading to structural defects arising from cycling and aging processes. Identifying these defects at an early stage is crucial to prevent service issues that could result in catastrophic failures. Hence, routine inspection and maintenance are crucial to prevent system collapse. To achieve this objective, conventional nondestructive testing (NDT) methods are utilized to i

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Publication Date
Sun Jun 03 2012
Journal Name
Baghdad Science Journal
On The Queuing System M/Er/1/N
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In this paper the queuing system (M/Er/1/N) has been considered in equilibrium. The method of stages introduced by Erlang has been used. The system of equations which governs the equilibrium probabilities of various stages has been given. For general N the probability of j stages of service are left in the system, has been introduced. And the probability for the empty system has been calculated in the explicit form.

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Publication Date
Tue Jan 08 2019
Journal Name
Iraqi Journal Of Physics
Effect of concentrations ratios of NiO on the efficiency of solar cell for (CdO)1-x(NiO)x thin films
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CdO:NiO/Si solar cell film was fabricated via deposition of CdO:NiO in different concentrations 1%, 3%, and 5% for NiO thin films in R.T and 723K, on n-type silicon substrate with approximately 200 nm thickness using pulse laser deposition. CdO:NiO/n-Si solar cell photovoltaic properties were examined under 60 mW/cm2 intensity illumination. The highest efficiency of the solar cell is 2.4% when the NiO concentration is 0.05 at 723K.

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Publication Date
Fri Dec 20 2019
Journal Name
College Of Islamic Sciences
The role of a teacher of Islamic education In explaining the concepts of political freedom Educational guidance study
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The political struggle being waged by Muslims today is one of the most important issues that have preoccupied the Arab and international media, and the failures that have afflicted Muslims in our contemporary world have negatively affected the younger generations and led them, and with the influence of anti-Islam media, to rely on accusing Islam as a religion with all the negative in Islamic and Arab society . So secularism took its role in spreading these concepts by deviating from its course from the concept of science to the concept of (the religion).
    From here the calls for reform rose to return the Muslims to the incubator of Islam, so people turned around them, but they turned into competing Islamic polit

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Publication Date
Tue Jun 01 2021
Journal Name
Political Sciences Journal
The role of elections in solidifying the process of democratization: a case study of Tunisian elections in 2019
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The electoral mechanism is remarkably clear, a political tool for institutional construction, directing political life, forming the political scene, and forming the partisan scene. This process was through the design of electoral laws, as elections in Tunisian political history represented the indicator of its slow and accelerated transformations, so The elections in Tunisia usually coincide with important political stages, accompanied by legislative or constitutional amendments in general, Islamic or secular forces have played a fundamental role in promoting the democratic experience and the principle of the peaceful transfer of power. This led to the formation of a national consensus that would help the country not enter into political

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Publication Date
Tue Jan 29 2019
Journal Name
Journal Of The College Of Education For Women
Begging Phenomenon Between the Destitution Plight and the Material Greedy - A Field Study in the City of Baghdad
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Begging is an ancient social phenomenon since the Man's creation. It was simple at its beginning to get a living and the family needed, but presently, this simple social phenomenon converted to a big phenomenon which controlled by competent groups away from the values and principles. Their doings are far from humanity representing by the cutting of a hand or a foot and facial distortion or removed eye as a way of attracting people's emotions to get material and incorporeal helps; these doings became a trade which is exchanged by slave traders. Furthermore, different illegal and greedy methods were followed as a way of blackmailing others; contrariwise other cases of begging are doing by a people who real poor and needy. In this case, the

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