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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 Nov 01 2013
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Treatment of chronic paronychia: A double blind comparative clinical trial using singly vaseline, nystatin and fucidic acid ointment
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KE Sharquie, AA Noaimi, SA Galib, Journal of Cosmetics, Dermatological Sciences and Applications, 2013 - Cited by 4

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Publication Date
Fri Nov 02 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Inducing the Health Promotion Model for Nursing Practice: Qualitative Study
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Objective: To generate a model that conceptualizes the phenomenon of health promotion and its related factors.
Methodology: A grounded theory methodology is used as qualitative method to explore the health promotion as
phenomenon of interest and its other related factors from the perspectives of specialists in this field. The study is
carried out from January 2002 through September 2004. A sample of (20) specialists in health sciences are
selected and interviewed as experts in the area of health promotion. The investigators conducted intensive and
structured interviews with the specialists to collect the data. These interviews were transcribed verbatim,
analyzed and interpreted.
Results: Findings of the study indicat

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Publication Date
Tue Jun 01 2010
Journal Name
Journal Of The College Of Languages (jcl)
Nature as a holy book
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Nature and natural beauty have always been the source of inspiration for poets and mystics.  For them, nature is one of the most recurrent and celebrated themes. It is a significant symbol of the beauty, righteousness and freshness they are looking for. For religious and mystical poets, it is a reference to God, his beauty, and splendour. Comparing it with the scripture, Thomas Ryan, a Catholic priest and a mystical writer, says ''The Bible is the 'small book', the world of nature is the 'big book'. Both reveal the Creator.''1

     For Muslim mystics, God does exist everywhere as the Qur'an states:   ''Wherever (Whithersoever)  you turn, there is God's face” (Chapter (Surah): 2

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Publication Date
Wed Apr 23 2025
Journal Name
Journal Of The College Of Basic Education
A historical study of Iraqi Olympic participation for the period (1929 - 2000)
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The history of the Olympic movement in Iraq is a rich history that reflects the interest of Iraqi governments and society in sports, the social and economic conditions, and international relations, and highlights the intersection of sports and politics and the impact of global events on local sports development. Therefore, providing a valuable insight into the reality of the participation and results achieved by Iraq in the Olympic Games for the period under study helps in giving a broader understanding of Iraq’s position in the global sports community. The research aims to document the important events in the development of the Olympic movement in Iraq for the period (1929-2000) and explore the formation and development of the Iraqi Olym

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Publication Date
Wed Jun 03 2020
Journal Name
Political Sciences Journal
The role of the strategic culture variable in negotiations (Brexit a model)
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      Negotiations are distinguished in that they are an easy and simple means between the conflicting parties, and it is an effective means at the same time as the conflicting parties seek understanding on the most effective way to solve their dispute, but negotiations are not always appropriate to resolve international disputes, especially when there is a disparity in power between the negotiating countries, or when it is missing Goodwill, or even when one of the parties is absent or less flexible, and the internal circumstances of one of the conflicting countries may play a negative or positive role in the success of the negotiations, away from the influence of the role of external variables in that, a

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Publication Date
Mon Dec 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Comparative Study of Pressure Losses and Hole Cleaning Efficiency of Water and Polymer solutions in Horizontal Wells
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The main objective of this study is to experimentally investigate the effect of the CMC polymeric drag reducer on the pressure drop occurred along the annulus of the wellbore in drilling operation and investigate the optimum polymer concentration that give the minimum pressure drop. A flow loop was designed for this purpose consist from 14 m long with transparent test section and differential pressure transmitter that allows to sense and measure the pressure losses along the test section. The results from the experimental work show that increasing in polymer concentration help to reduce the pressure drop in annulus and the optimum polymer concentration with the maximum drag reducing is 0.8 kg/m3. Also increasing in flow rate a

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Publication Date
Thu Jun 16 2022
Journal Name
Comparative Parasitology
A Comparative Study of Some Intestinal Parasites in Fecal Samples of Domestic and Stray Cats in Baghdad, Iraq
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Some feline intestinal parasites such as Toxocara, Giardia, and Cryptosporidium can spread to humans through feces. Therefore, it is important to prevent exposure of family members by screening cat fecal samples twice per year for potential treatment regimes. This study was initiated to compare and identify gastrointestinal parasites of domestic and stray cats (Felis domesticus) in Baghdad City, Iraq. Parasite eggs and oocysts were identified under light microscopy by applying standard laboratory techniques (flotation and sedimentation). Overall, 59 of 121 (48.7%) fecal samples were positive for intestinal parasites. The rate of infection by Toxoplasma gondii was (3.31%), Isospora spp. (6.61%), Cryptosporidium spp. (31.4%), and Toxocara spp

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Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Us-china Public Administration
Victims of Terrorism between Compensation and Loss of Rights: A Comparative Study between Iraqi Law and French Law
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The problem of the damage caused by terrorist acts has raised many difficulties in many countries, including Iraq, which requires the existence of a law that sets out sufficient rules for compensating the victims of terrorist acts, in order to compensate them for the harm they have not suffered. It may be difficult or impossible for them to identify causing damage, and therefore unable to obtain compensation by applying the traditional rules of liability that require proof of fault and identify the culprit. The security funds come as an appropriate alternative that pays compensation in such cases for victims to reparation for the damage they suffered. Therefore, this problem remains one of the most problems that Iraq suffers from it, which

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Publication Date
Tue Jun 30 2020
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Reuse of Brick Waste as a Cheap-Sorbent for the Removal of Nickel Ions from Aqueous Solutions
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   The potential application of granules of brick waste (GBW) as a low-cost sorbent for removal of Ni+2ions from aqueous solutions has been studied. The properties of GBW were determined through several tests such as X-Ray diffraction (XRD), Energy dispersive X-ray (EDX), Scanning electron microscopy (SEM), and BET surface area. In batch tests, the influence of several operating parameters including contact time, initial concentration, agitation speed, and the dose of GBW was investigated. The best values of these parameters that provided maximum removal efficiency of nickel (39.4%) were 1.5 hr, 50 mg/L, 250 rpm, and 1.8 g/100mL, respectively. The adsorption data obtained by batch experiments subjected to the Three i

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Publication Date
Mon Jan 13 2020
Journal Name
Day 3 Wed, January 15, 2020
Numerical Simulation of Gas Lift Optimization Using Genetic Algorithm for a Middle East Oil Field: Feasibility Study
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<p>Gas-lift technique plays an important role in sustaining oil production, especially from a mature field when the reservoirs’ natural energy becomes insufficient. However, optimally allocation of the gas injection rate in a large field through its gas-lift network system towards maximization of oil production rate is a challenging task. The conventional gas-lift optimization problems may become inefficient and incapable of modelling the gas-lift optimization in a large network system with problems associated with multi-objective, multi-constrained, and limited gas injection rate. The key objective of this study is to assess the feasibility of utilizing the Genetic Algorithm (GA) technique to optimize t</p> ... Show More
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