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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
Sat Jul 01 2017
Journal Name
Al–bahith Al–a'alami
The effects of Internet use on university’s students: “A Study on a Sample of Jordanian University’s students "
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The effects of Internet use on university’s students:The effects of Internet use on university’s students:“A Study on a Sample of Jordanian University’s students "This survey aims to identify the most important effects of Internet use on Jordanian public and private universities’ students by monitoring and analyzing a set of indicators that show the quality of the effects on specific fields such as  cultural, social, psychological, moral and political effects .To achieve these goals, the study attempts to answer the following questions:1.   What are the effects of Internet’s use on students?2. What is   the relationship between the effects and demographic variables such as  gender, age, family size an

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Publication Date
Fri Nov 01 2019
Journal Name
Science International (lahore)
IRAQI WOMEN IN THE CIRCLE OF COMBATTING A STUDY OF CIVIL-MILITARY RELATIONS IN A GENDER PERSPECTIVE
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The current research includes a look at the participation of Iraqi women in the combat roles, which starts from the assumption of the democratic transition that must be led - in one of its aspect - until the army or the military foundation to become a "citizen army," the matter which is represented a demand increasingly needed in the experiences of Democratic transformation that facing serious security challenges such as in Iraq, this means that the army or security foundation - which is involved in counterterrorism - should not reflect a specific group in society , and hence embody the most important democratic principles, which are equality and equal opportunities, especially gender equality. On the other hand, the influence of armed conf

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Publication Date
Sun Jan 08 2023
Journal Name
Journal Of Planner And Development
Design bases for waste recycling rules in cities/ Baghdad, a case study"
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Waste is one of the most important problems affecting the city’s environment and its urban landscape, which results from the activities and activities of man and the natural environment. Its sources have varied between residential, commercial, industrial, medical and hazardous, and its spread in cities, on roads and on abandoned open lands, has led to significant negative effects and risks to human health and the environment.

  Therefore, there were serious attempts to deal with waste and follow sequential steps that formed a waste management system such as (collection, sorting, transport, then treatment and disposal). Preventing and reducing waste, then recycling and recovering by composting or burning, and ending with bu

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Publication Date
Tue Jun 20 2023
Journal Name
Baghdad Science Journal
Assessment of image quality of cervical spine complications using Three Magnetic Resonance Imaging Sequences
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Examining and comparing the image quality of degenerative cervical spine diseases through the application of three MRI sequences; the Two-Dimension T2 Weighed Turbo Spin Echo (2D T2W TSE), the Three-Dimension T2 Weighted Turbo Spin Echo (3D T2W TSE), and the T2 Turbo Field Echo (T2_TFE). Thirty-three patients who were diagnosed as having degenerative cervical spine diseases were involved in this study. Their age range was 40-60 years old. The images were produced via a 1.5 Tesla MRI device using (2D T2W TSE, 3D T2W TSE, and T2_TFE) sequences in the sagittal plane. The image quality was examined by objective and subjective assessments. The MRI image characteristics of the cervical spines (C4-C5, C5-C6, C6-C7) showed significant difference

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Publication Date
Fri Apr 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The Committed of the Auditors for the Procedures of Environmental audits (An Exploratory Study of a sample of auditing offices in Iraq)
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At the beginning of the nineties increased responsibility of the auditor to the community as the demand for auditing the environmental performance for the economic units in addition to audit the financial performance. With the aim of preserving the environment and reducing the damagse as  aresult of the negative effects of the activities of these units.

The researh deal with two sides the first one identifies the theoretical framework of the concept of environmental audits, requirements, methods, types of procedures, and duties of  the auditor in conducting  environmental audits. It also deals with the concept of the enviro

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Publication Date
Fri Nov 21 2025
Journal Name
Al-anbar University Journal Of Law And Political Sciences
The Effect of E-Government on Public Facility Management Methods (Comparative Study)
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Publication Date
Wed Jun 29 2022
Journal Name
Journal Of The College Of Education For Women
The Chicago School in Urban Sociology: A Socio-Historical Approach on the Pragmatic Thought Influence as a Theoretical Frame of Reference in it-1892-2020
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The present theoretical study analyzes the legacy of the Chicago School of Urban Sociology and evaluates it in the light of the growth and development of Chicago City and the establishment of sociology in it. Sociology has become an academic discipline recognized in the United States of America in the late nineteenth century, particularly, after the establishment of the first department of sociology in the University of Chicago in 1892. That was during the period of the rapid industrialization and sustainable growth of the Chicago City. The Chicago School relied on Chicago City in particular, as one of the American cities that grew and expanded rapidly in the first two decades of the twentieth century. At the end of the nineteenth centur

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Publication Date
Mon Mar 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
The study of the effect of the use of programming in the linear programming model (applied study)
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The parametric programming considered as type of sensitivity analysis. In this research concerning to study the effect of the variations on linear programming model (objective function coefficients and right hand side) on the optimal solution. To determine the parameter (θ) value (-5≤ θ ≤5).Whereas the result، the objective function equal  zero and the decision variables are non basic، when the parameter (θ = -5).The objective function value increases when the parameter (θ= 5) and the decision variables are basic، with the except of X24, X34.Whenever the parameter value increase, the objectiv

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Publication Date
Fri Nov 21 2025
Journal Name
Al–bahith Al–a'alami
The Reliance of the Public of Baghdad on News Broadcasts on Satellite Channels as a Source of Information
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The importance of news broadcasts in society has increased after the domination of television over the mass media, especially after emerging the satellite channels, and spreading the satellite dishes among the public at large.

As well as the great role played by the modern technology in the transmission of news and events happening at once. Such role has contributed, significantly, in changing the concept and values ​​of the news. The live broadcast of the events filmed is the news itself.

In the midst of the great transformations and circumstances that Iraq went through after 2003, which witnessed political and security instability, and the large increase in the number of media, especially satellite channels, in Iraq

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Publication Date
Wed Jun 27 2018
Journal Name
Iraqi Journal Of Science
Accurate Three Dimensional Coordinates Measurements Using Differential GPS Real Time Kinematic Mode
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The accurate 3-D coordinate's measurements of the global positioning systems are essential in many fields and applications. The GPS has numerous applications such as: Frequency Counters, Geographic Information Systems, Intelligent Vehicle Highway Systems, Car Navigation Systems, Emergency Systems, Aviations, Astronomical Pointing Control, and Atmospheric Sounding using GPS signals, tracking of wild animals, GPS Aid for the Blind, Recorded Position Information, Airborne Gravimetry and other uses. In this paper, the RTK DGPS mode has been used to create precise 3-D coordinates values for four rover stations in Baghdad university camp. The HiPer-II Receiver of global positioning system was used to navigate the coordinate value. The results wil

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