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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 Jan 01 2023
Journal Name
Studies In Systems, Decision And Control
Gap Analysis by Readiness Review Including Online Learning During COVID-19 Pandemic Period for Engineering Programs at the College of Engineering—University of Baghdad
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Publication Date
Sun Dec 10 2023
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Detection of Multiple Sclerosis Lesions in Supra- and Infra-Tentorial Anatomical Regions by Double Inversion Recovery, Flair, and T2 MRI Sequences: A Comparative Study in Iraqi Patients
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Background: In young adults, multiple sclerosis is a prevalent chronic inflammatory demyelinating condition. It is characterized by white matter affection, but many individuals also have significant gray matter involvement. A double-inversion recovery pulse (DIR) pattern was recently proposed to improve the visibility of multiple sclerosis lesions. Objective: To find out how well a DIR sequence, FLAIR, and T2-weighted pulse sequences can find MS lesions in the supratentorial and infratentorial regions. Methods: A total of 37 patients with established diagnoses of multiple sclerosis were included in this cross-sectional study. Brain MRI was done using double inversion recovery, T2, and FLAIR sequences. The number of lesions was count

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
What came as a language in the book to explain Ibn Aqeel on Alfiya Ibn malek
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It is found in the book "Ibn Aqeel: Alfiya Ibn Malek" that there are some linqustical aspected are related to the native tribal speakers like Tamim or Tie or some others. Sometimes in the book he said "some Arabian said without mentioning the name of the tribe.
As weel, he hasn’t mentioned the accent but he does mention the language. In the book, he has brought back the most important and the biqqest Arabian tribes suchas tribes of Hegaz, Tamim, Hatheyal, son of Anber, Tie, Rabia Bin Wael, Bani Katham, Au there, Bani AL Harth, Bani Kalb, Bani Hgim, Zabid, Hamedan, Alia Qais, Bani Ameer and many others. However, the most mentioned tribes were Hegaz and Tami.
Hence, the importance of the book expiain Ibn Aqeel by mentioning these A

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Publication Date
Tue Apr 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Organizational citizenship behaviors under theory of servant leadership: A exploratory study in a sample of faculties of the University of Alqadisiya
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This study aimed to identify the role of servant leadership in promoting organizational citizenship behaviors in a sample of faculties of the University of Alqadisiya .It tried to answer several questions represented its problem.

 

 The most important questions are the followings:

1- Is there enough perception among administrative leaders in the aforementioned faculties toward the concept of servant leadership? And under what level?                                    &

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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
Sun Jan 27 2019
Journal Name
Civil Engineering Journal
Prediction of Sediment Accumulation Model for Trunk Sewer Using Multiple Linear Regression and Neural Network Techniques
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Sewer sediment deposition is an important aspect as it relates to several operational and environmental problems. It concerns municipalities as it affects the sewer system and contributes to sewer failure which has a catastrophic effect if happened in trunks or interceptors. Sewer rehabilitation is a costly process and complex in terms of choosing the method of rehabilitation and individual sewers to be rehabilitated.  For such a complex process, inspection techniques assist in the decision-making process; though, it may add to the total expenditure of the project as it requires special tools and trained personnel. For developing countries, Inspection could prohibit the rehabilitation proceeds. In this study, the researchers propos

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Publication Date
Sat Dec 31 2022
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of Robust Circular S and Circular Least Squares Estimators for Circular Regression Model using Simulation
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In this paper, the Monte-Carlo simulation method was used to compare the robust circular S estimator with the circular Least squares method in the case of no outlier data and in the case of the presence of an outlier in the data through two trends, the first is contaminant with high inflection points that represents contaminant in the circular independent variable, and the second the contaminant in the vertical variable that represents the circular dependent variable using three comparison criteria, the median standard error (Median SE), the median of the mean squares of error (Median MSE), and the median of the mean cosines of the circular residuals (Median A(k)). It was concluded that the method of least squares is better than the

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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
Mon Jan 01 2001
Journal Name
University Of Jordan
A Study of Some Generalizations of Proper Mappings
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Publication Date
Mon May 01 2023
Journal Name
Journal Of Molecular Liquids
On the influence of hydrocarbons solvents on the inhibition efficiency of some organic corrosion inhibitors: Theoretical and validation studies
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