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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 Sep 30 2012
Journal Name
College Of Islamic Sciences
Surat Al-Qaria: a linguistic study
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Praise be to God, Lord of the worlds, and the best of prayers, and extradition was made to our master Muhammad and his whole family and companions:
And after:
Surat Al-Qariah is from the royal fence, which is in the thirtieth part of the Noble Qur’an. The commentators differed on the number of verses, and the reason for its naming. This surah talked about the conditions of people on the Day of Resurrection, and about how people were removed from their graves, all of which I spoke about in the preamble.
The research is divided into six topics: the first topic dealt with strange terms, while the second topic dealt with the most important audio issues mentioned in the surah, namely (slurring, advertising, substitution, and silenc

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Publication Date
Mon Jun 28 2021
Journal Name
Journal Of Engineering
Effective quality control of a municipal wastewater treatment plant using Geographic information systems: A Review
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Inefficient wastewater disposal and wastewater discharge problems in water bodies have led to increasing pollution in water bodies.  Pollutants in the river contribute to increasing the biological oxygen demand (BOD), total suspended solids (SS), total dissolved solids (TDS), chemical oxygen demand (COD), and toxic metals render this water unsuitable for consumption and even pose a significant risk to human health. Over the last few years, water conservation has been the subject of growing awareness and concern throughout the world, so this research focused on review studies of researches that studied the importance of water quality of wastewater treated disposal in water bodies and modern technology to management w

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Publication Date
Fri Jun 03 2022
Journal Name
Military Medical Science Letters
COVID-19 AMONG A SAMPLE OF IRAQI PATIENTS WITH RHEUMATIC DISEASES: A MULTICENTER STUDY
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Publication Date
Sun Mar 06 2016
Journal Name
Baghdad Science Journal
A study of Soil Invertebrates community in a Date - Palm plantation in Baghdad, Iraq
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Soil invertebrates community an important role as part of essential food chain and responsible for the decomposition in the soil, helps soil aeration , nutrients recycling and increase agricultural production by providing the essential elements necessary for photosynthesis and energy flow in ecosystems.The aim of the present study was to investigate the soil invertebrates community in one of the date palms plantation in Aljaderia district South of Baghdad, , and their relationships with some physical and chemical properties of the soil , as Five randomly distributed replicates of soil samples were collected monthly. Invertebrates samples were sorted from the soil with two methods, direct method to isolate large invertebrates and indirec

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Publication Date
Thu Sep 17 2020
Journal Name
College Of Islamic Sciences
Human values and principles in the three religions
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The laws of the three religions tend to extend the rules and foundations of coexistence, and this is achieved in achieving the values and principles that these laws have nourished in all societies.

Our research deals with a major problem that has broken out in our societies, namely (disturbing the balance of values and behavioral standard between people), and perhaps one of the greatest causes of the problem is to move away from the correct divine discourse and sound approach, as well as corruption of common sense and the violation of its rules and found principles in the hearts of people.

 

 

 

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Publication Date
Sun Dec 01 2024
Journal Name
Baghdad Science Journal
Synthesis, Characterization and Antioxidant Study of Some Metal Ion Complexes with Azo 1-(2,4,6-trihydroxy-3-((3-hydroxyphenyl) diazenyl) phenyl) Ethan-1-one.
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اثناء تفاعل الديزنة تكونت صبغة أزو جديدة عن طريق تفاعل 3-امينوفينول مع 2,4,6-ثلاثي هيدروكسي اسيتوفينون . ثم تم تفاعل هذا الليكاند مع بعض ايونات العناصر الكروم والحديد الروديوم والروثينيوم بتكفؤهم الثلاثي والكوبلت الثنائي والموليبدينوم سداسي التكافؤ مكونة معقدات فلزية مختلفة بأشكال هندسية متعددة. تم ملاحظة تناسق مجموعة الازو مع ايونات العناصر من خلال ملاحظة ظهور حزم امتصاص الفلز مع النتروجين والاوكسجين ب

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The effect of Layout in measuring customer satisfaction (patients) using (Servicescape) model
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Abstract:

This research aims to identify the impact of the Layout Ghazi al-Hariri hospital for surgery specialist on customer satisfaction (patients) using the model (Servicescape), the problem of the research represented in the extent to which the hospital management design of the service and Layout hospital aesthetic and functional aspects that fit patients for therapeutic and nursing services , and used the developer scale by (Miles et al., 2012) for data collection, which includes the independent variable in (17) items distributed in three dimensions (Facility aesthetics , hospital cleanliness, and the Layout accessibility ) The dependent variable is the satisfaction of customers (pat

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Publication Date
Wed Dec 25 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Non-interest income and its impact on the profits of the Iraqi banking sector: (Comparative study)
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     In this study,  has been discussed the issue of non-interest income and its impact on the Iraqi banking sector profit for the period between (2008-2017) as it was the main objective of the study is to find the relationship between the non-interest income and the profits of the banking sector in order to know  the size of the sector's dependence on non-interest income As well as an analysis of its profitability compared to selected countries, And to test hypotheses, the financial ratios and some statistical tests to determine the stability of the time series such as the test (Correlegram , Dickey -Fuller (depending on the statistical program (E-Views V8) and a simple linear regression method by (Minitab

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Publication Date
Sun Jun 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A study of the Rate of Sedimentation of Magnesium Hydroxide Obtained from Bittern
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Publication Date
Thu Oct 18 2018
Journal Name
Al–bahith Al–a'alami
Watching Cultural Programs in Satellites Channels tv and Its relation to the actual reading of the book
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The research is based on an important subject according to the researchers' estimations. It is the disclosure of the nature of the relationship between Watching to cultural programs in satellite channels and the book's vision of the intellectual, and the pursuit of purchasing and acquiring it It is a scientific addition to the scientific research media because it deals in the field of new about the nature of the relationship between satellite programs and writers, and it provides a scientific development on the importance of satellite channels in the promotion of the book and sales of intellectual elite. The study examined the audience of the recipients of literature for cultural programs, the nature of the public, characteristic

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