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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 Feb 24 2019
Journal Name
Iraqi Journal Of Physics
Comparison of three interpolation methods for the average monthly temperature in the south of Iraqi zone
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This study focuses on evaluating the suitability of three interpolation methods in terms of their accuracy at climate data for some provinces of south of Iraq. Two data sets of maximum and minimum temperature in February 2008 from nine meteorological stations located in the south of Iraq using three interpolation methods. ArcGIS is used to produce the spatially distributed temperature data by using IDW, ordinary kriging, and spline. Four statistical methods are applied to analyze the results obtained from three interpolation methods. These methods are RMSE, RMSE as a percentage of the mean, Model efficiency (E) and Bias, which showed that the ordinary krigingis the best for this data from other methods by the results that have b

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Publication Date
Wed Sep 29 2021
Journal Name
College Of Islamic Sciences
The provisions of the epidemic in jurisprudence and its principles The (Covid-19) epidemic is a model
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Abstract

Epidemics that afflict humankind are descending renewed, plaguing them in the place and time they spread.

- The epidemic affects individuals and the movement of societies, and its treatment requires dealing with it according to Sharia, taking into account the current data and developments.

- Integrative jurisprudence: it is intended to know the practical legal rulings deduced from the combination of evidence of two or more sciences related to one topic related to it, and among these calamities is the Corona Covid-19 pandemic.

 - It is permissible to use sterile materials that contain a percentage of alcohol in sterilizing hands and fogging places, including mosques.

T

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Publication Date
Sun Sep 30 2018
Journal Name
الجامعة المستنصرية كلية الإدارة و الاقتصاد
The possibility of adoption of hybrid cloud computing in Iraqi universities : an analytical study using technology acceptance model
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الناصر، عامر عبد الرزاق عبد المحسن والكبيسي، صلاح الدين عواد كريم. 2018. إمكانية تبني الحوسبة السحابية الهجينة في الجامعات العراقية : دراسة تحليلية باستخدام أنموذج القبول التكنولوجي. مجلة الإدا

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Publication Date
Mon Mar 25 2019
Journal Name
Al-academy
Time in the Cinema...The Two Films (The Knife and The Deceived) -A Model: كريمة ناوي
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This study deals with the time property in the cinema through two films: (The Knife) directed by Khalid Hamada and (The Deceived) directed by Tawfiq Saleh. These two films were excerpted by the cinema from two novels of the Palestinian writer Ghassan Kanafani, the first is from the novel (What is Left for You) and the second is from the novel (Men in the Sun).  If the Palestinian novel has imposed its presence on the Arab creative scene through a group of novelists who took it upon themselves to communicate their cause to the world,   the Palestinian cinema has been far from being a purely Palestinian, because many of the cinematic works have been provided by Arab countries on the issue, while this cinema is still seeking

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison Between Some Estimator Methods of Linear Regression Model With Auto-Correlated Errors With Application Data for the Wheat in Iraq
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This research a study model of linear regression problem of autocorrelation of random error is spread when a normal distribution as used in linear regression analysis for relationship between variables and through this relationship can predict the value of a variable with the values of other variables, and was comparing methods (method of least squares, method of the average un-weighted, Thiel method and Laplace method) using the mean square error (MSE) boxes and simulation and the study included fore sizes of samples (15, 30, 60, 100). The results showed that the least-squares method is best, applying the fore methods of buckwheat production data and the cultivated area of the provinces of Iraq for years (2010), (2011), (2012),

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Publication Date
Tue Feb 18 2025
Journal Name
Plasmonics
A Partial Least Squares (PLS2) Model Based on Kinetic-Spectrophotometric Measurement for the Simultaneous Determination of Tetracycline and Phenylephrine in Binary Mixtures
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Publication Date
Fri Oct 04 2024
Journal Name
Chemical Review And Letters
Newly designed 2-(aminomethyl)benzimidazole derivatives as possible tyrosine kinase inhibitors: synthesis, characterization, preliminary cytotoxic evaluation and in Silico studies
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Publication Date
Fri Jun 01 2018
Journal Name
Iraqi Journal Of Science
Cleavage of mucin and salivary agglutinin by partiallypurified protease from native strain of Streptococcus mutansan67
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Publication Date
Mon Jan 01 2024
Journal Name
Lecture Notes In Electrical Engineering
A Study of the Influence of Steel Brushes in Rail Surface Magnetic Flux Leakage Detection Using Finite Elements Simulation
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Publication Date
Mon Feb 25 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Impact of Using the Information Technology on The Audit Profession: A Study of the Sample of Auditor Viewpoints in Selected Arab Countries
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This study aims to clarify areas of using information technology in accounting and its impact on the profession of auditors by reviewing the concept, types, areas and the importance of information technology and its implications on the audit profession as well as to clarify the extent of contribution of information technology in  developing of procedures of the audit profession and what its requirement, also this study aims to enhance the theoretical side by identifying the views of a sample of auditors in  Arab countries selected (Iraq, Syria, Jordan), for the extent of using of information technology in their work and level of their perception for the importance of that

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