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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 Oct 01 2023
Journal Name
Baghdad Science Journal
Molecular detection by some virulence genes of Salmonella enterica subsp. enterica isolated from the stool of children with diarrhea
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Diarrhea is a real disease in childhood which could cause death. Therefore, this study was conducted to isolate Salmonella from 350 stool samples taken from children under five years in age, suffering from diarrhea during the period from March 2019 to March 2020 in Tikrit city / Iraq. The results showed the possibility to isolate ten isolates of Salmonella enterica subsp. Enterica, an infection rate, represents 2.875% of the total rate of patients who suffer from diarrhea. The virulence genes were investigated for ten isolates of S. enterica subsp. enterica, the result is that all isolates possessed the genes stn, invA, lpfA with an appearance percentage of 100%, whi

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Publication Date
Tue Dec 19 2023
Journal Name
Bulletin Of The Iraq Natural History Museum
MORPHOLOGICAL AND MOLECULAR STUDIES OF KAIS KINGFISH CYPRINION KAIS HECKEL, 1843 (PISCIES, CYPRINIFORMES, CYPRINIDAE) FROM THE MIDDLE OF IRAQ
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Cyprinidae species are the most abundant and widely distributed fish species in the inland waters of Iraq. Cyprinids are complex species, and it is difficult to identify them on the basis of morphology. Thus, the morphological characteristics must be achieved and confirmed by molecular analysis. Twenty specimens of Cyprinion kais Heckel, 1843 (Piscies, Cypriniformes, Cyprinidae) were collected from two localities at Tigris River in the middle of Iraq: five specimens from Al-Tharthar Lake, Saladin Province, and 15 specimens from Al- Zubaydiyah sub-district, Wasit Province. The DNA sequences of C. kais were done using the mitochondrial DNA cytochrome b (cytb) gene. After analysis, the sequences were compared with sequences of ot

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Educational And Psychological Researches
The factors that affecting in the recruitment of a teaching staff for the Massive Open Online Courses (MOOCs) in university teaching at the University of Khartoum.
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This research aimed at identifying the factors that affecting in the recruitment of a teaching staff for the Massive Open Online Courses (MOOCs) in university teaching at the University of Khartoum. The descriptive method was followed. The questionnaire was used as a tool for data collection,, which was distributed directly to a sample of (181) respondent of the teaching staff members of the senate at University of Khartoum from those who were attend at the senate meeting No. (409) which was held on 22 August 2016 Of (272). The researcher followed for the distribution the chance method, where each questionnaire was distributed to each of a teaching staff from different faculties at the University of Khartoum, according to his willingness

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Publication Date
Tue Mar 30 2021
Journal Name
Iraqi Journal Of Science
Electrochemical Polymerization and Biological Activity of 4-(Nicotinamido)-4-Oxo-2-Butenoic Acid as An Anticorrosion Coating on A 316L Stainless Steel Surface
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In this study, poly4-(nicotinamido)-4-oxo-2-butenoic acid (PNOE) was prepared by the electro polymerization of 4-(nicotinamido)-4-oxo-2-butenoic acid (NOE) monomer on a 316 stainless steel (St.St) which acts as an anticorrosion coating.  Fourier transforms infrared (FTIR), atomic force microscopy (AFM), scanning electron microscopy (SEM), and cyclic voltammetry were used to diagnose the structure and the properties of the prepared polymer layer. The corrosion behavior of the uncoated and coated 316  St.St were evaluated by using an electro chemical polarization technique in 0.2 M hydrochloric acid  solution as a corrosive medium at a temperature range of 293 to 323 K. Nano materials, such as nano ZnO and graphene were added in di

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Publication Date
Sat Jun 04 2022
Journal Name
Al–bahith Al–a'alami
The Media Image of Afghan Women as Reflected by News Websites in 2021: an Analytical Study of Russia Today site
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International news websites, including Russia Today, pay special attention to the media image of Afghan women, especially after the Taliban movement took control of Afghanistan. Therefore, it was necessary to know the image of the Afghan woman, the fate of the rights she acquired in recent years, and the transformations that affected her after the Taliban took control of the government, and studied them on international news sites, specifically Russia Today.

          The researcher summarized the problem of this study in the following question: What is the media image of the Afghan woman on the Russia Today news site?

         

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Study of weathering effect on the thermal conductivity of polyvinyl chloride before and after silicon carbide addition as packaging materials
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The work was carried out in two stages. The first stage concerned
with study of silicon carbide (SiC) ratio (1.5, 2.5, 3.5, and 4.5 wt%)
effect on the Thermal conductivity of polyvinyl chloride (PVC); and
the second stage concerned with the UV – weatherizing (25, 50, and
75 hr), thermal aging (40, 50, and 60 °C), and rain- weatherizing (1,
2.5, and 4 hr) effect on the samples involved. Thermal conductivity
results proved that there was slight increase in thermal conductivity
by (SiC) loading; it increased from 0.17 W/m.K for PVC to 0.19
W/m.K for 4.5% SiC/PVC; where as it was systematically decreased
by UV- weatherizing, thermal aging, and rain- weatherizing. This
property is in a good agreement with gene

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Publication Date
Mon Nov 24 2025
Journal Name
Al–bahith Al–a'alami
The Problemic of the ambiguous relationship between the media and terrorism, and the problems arising from… An exploratory study of a sample of journalists, writers and researchers in Baghdad
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This study examined the problematic of the ambiguous relationship between the media and terrorism and the problems that result from press coverage of terroristic incidents. The paper sought to show the classification and confrontation of such incidents had been established from the point of view of a sample of media professionals, researchers and writers who are frequenters of Al-Mutanabi Street in Baghdad. The media outlets that carry this coverage would not give up their media mission as well as the terrorists would not be given an opportunity to take advantage of this coverage in achieving their goals and objectives. Furthermore, the terrorist organizations would have no chance to exploit these means to deliver their terroristic messa

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Publication Date
Sat Apr 25 2020
Journal Name
International Journal Of Research In Social Sciences And Humanities
THE EFFECT OF CAPITAL ADEQUACY AND ASSET QUALITY ON THE VALUE OF THE BANK AN APPLIED STUDY ON A SAMPLE OF IRAQI BANKS LISTED ON THE IRAQ STOCK EXCHANGE
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As the banking sector is a strong influence on the country's economic growth,The solid financial well-being of anybank does not mean only a guarantee for its investors, It is also important for both owners and workers and for theeconomy in all its joints.The elements of capital adequacy and quality of assets are important to the functioning of thebanking business.In this study, the research sample included four private banks. Quarterly data were used for the period(2011 - 2018).Moreover, data is also collected from articles, papers, the World Wide Web (the Internet) and specializedinternational journals.In this research, an effort was made to try to find out the effect of (the ratio of the capital owned todeposits on the value of the bank),

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of American Science
Morphohistological study of the tongue in local mice species by using special stain
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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Physics: Conference Series
Study the Electronic Properties of Boron Nitride Diamondiod Nanostructure using Ab-initio DFT
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