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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 Jun 01 2015
Journal Name
Int. J. Adv. Appl. Math. Andmech.
The effect of external source of disease on the epidemic model
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Publication Date
Sun Sep 07 2014
Journal Name
Baghdad Science Journal
Exponential Function of a bounded Linear Operator on a Hilbert Space.
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In this paper, we introduce an exponential of an operator defined on a Hilbert space H, and we study its properties and find some of properties of T inherited to exponential operator, so we study the spectrum of exponential operator e^T according to the operator T.

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
PRESS COVERAGE OF CRISES: (A Research Drawn from a Doctoral Thesis)
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Media is one of the main and effective factors; and it is a tool of crisis management equipment. Media is one of the most dangerous, effective and decisive weapons in modern conflicts; a tool for making events and influencing their events and trends as a means of reporting as the enormous capabilities of media which help media to move very quickly, and cross borders; and overcome obstacles, through many means of audio, reading and visual. As its ability, moreover, to influence the psychological and intellectual control of communities, and behaviors.

Intelligent media is, then, used in crises management and coverage. Crises have been existed with the presence of man on Earth. Thei

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Publication Date
Mon Aug 01 2022
Journal Name
Communications In Mathematical Biology And Neuroscience
Stability analysis of a competitive ecological system in a polluted environment
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The interplay of species in a polluted environment is one of the most critical aspects of the ecosystem. This paper explores the dynamics of the two-species Lokta–Volterra competition model. According to the type I functional response, one species is affected by environmental pollution. Whilst the other degrades the toxin according to the type II functional response. All equilibrium points of the system are located, with their local and global stability being assessed. A numerical simulation examination is carried out to confirm the theoretical results. These results illustrate that competition and pollution can significantly change the coexistence and extinction of each species.

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Publication Date
Tue Dec 20 2022
Journal Name
Journal Of Language Studies
A Rhetorical Analysis of Fallacy in a Selected English Drama Movie
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Fallacies are incorrect reasoning that make an argument seem less logically credible and easier to be identified as unsound. They are widespread; individuals commit them while engaging in various activities, including at work, at home, while creating advertisements, and in the media. This study aims to investigate the rhetorical strategies accompanied with producing the fallacious arguments selected from the American Film “12 Angry Men (1957)”. The study adopts Damer’s (2009) model for the identification of fallacy. As for rhetorical analysis, the study adopts Aristotle’s triangle of rhetoric and McGuigan’s (2007) taxonomy of rhetorical devices. The results uncover that the most violated criteria are relevance, acceptabili

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Publication Date
Fri Dec 11 2020
Journal Name
2020 Ieee 8th Conference On Systems, Process And Control (icspc)
A Survey of Different DC Faults in a Solar Power System
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Publication Date
Wed Jul 01 2015
Journal Name
Al–bahith Al–a'alami
Favorite TV Channels / as News Sources for Iraqi University Professors.
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The growing ability of Television to transfer and present events as they occur and sometimes transfer events alive makes it the most important sources to receive news and find out what is going on in the world. These channels form the importance of multiple sources and displayed content, especially news. What adds to the importance of the research is that the people under study are Iraqi professors
The problem of the study is represented by an essential inquiry about the favorite satellite channels to obtain news for Iraqi professors
The aims of the study are identified by finding out the most favorite satellite channels as a source of news for Iraqi professors and the habits of exposer to the news by them
The research is a des

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Publication Date
Thu Apr 21 2022
Journal Name
Journal Of Petroleum Research And Studies
Smart Well Modelling for As Reservoir in AG Oil Field
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Intelligent or smart completion wells vary from conventional wells. They have downhole flow control devices like Inflow Control Devices (ICD) and Interval Control Valves (ICV) to enhance reservoir management and control, optimizing hydrocarbon output and recovery. However, to explain their adoption and increase their economic return, a high level of justification is necessary. Smart horizontal wells also necessitate optimizing the number of valves, nozzles, and compartment length. A three-dimensional geological model of the As reservoir in AG oil field was used to see the influence of these factors on cumulative oil production and NPV. After creating the dynamic model for the As reservoir using the program Petrel (2017.4), we

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Publication Date
Sun Jun 03 2018
Journal Name
Baghdad Science Journal
Diamine Derivatives as Photostabilizers for Thermoplasticized Poly(Vinyl Chloride) [I]
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The photostabilization? of poly vinyl chloride (PVC) ? films has been investigated by using diamine derivatives. The? (PVC) films were? contained 0.5% weight? of diamine derivatives which prepared by the method of casting. The photostabilizations? ?of these compounds were determined by monitoring the carbonyl index value with irradiation time. Also, the effect ?of concentrations of additives (range 0.1-0.5wt) on the rate of photostabilization? process was studied. Therefore we found? that a increased photostabilization rates was increase with increasing? concentrations of compound. Besides, the influence? on film thickness? of photostabilization process was also studied; ?and the results? showed that? the increasing of film thickness incr

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Publication Date
Wed Dec 30 2009
Journal Name
Iraqi Journal Of Physics
CuInS2 Ternary Compound as Absorption Layer for Solar Cell Fabrication
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Copper indium disulphide, CuInS2, is a promising absorber material for thin film photovoltaic which has recently attracted considerable attention due to its suitability to reach high efficiency solar cells by using low cost techniques. In this work CuInS2 thin films have been deposited by chemical spray pyrolysis onto glass substrates at ambient atmosphere, using different [Cu]/[In] ratio in the aqueous solutions at substrate temperature 3000C
and different annealing temperatures . Structural and optical properties of CIS films were analyzed by X-ray diffraction, and optical spectroscopy. Sprayed CIS films are polycrystalline with a chalcopyrite structure with a preferential orientation along the 112 direction and no remains of oxides

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