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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
Mon Jan 01 2024
Journal Name
Journal Of Oral Medicine And Oral Surgery
Evaluating dental implant stability using three devices Osstell<sup>®</sup>, Periotest<sup>®</sup>, and AnyCheck<sup>®</sup>: a clinical study
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Introduction: Implant stability is usually measured with resonance frequency analysis (RFA) and damping capacity assessment (DCA). This study aimed to measure primary and secondary stabilities using 3 devices that are based on these methods, namely; RFA (Osstell®) and DCA (Periotest® and AnyCheck®) to assess the correlations of the measurements obtained by these devices and the correlations between implant stability and insertion torque. Material and Methods: This observational prospective study included 35 dental implants. The implant stability was measured using the 3 devices. Mann–Whitney U

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Publication Date
Mon Feb 16 2026
Journal Name
Journal Of Baghdad College Of Dentistry
A comparative study to evaluate the shear bond strength of different resin sealers to dentin (An in vitro study)
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Background: One of the major problems in endodontics is micro-leakage of root canal fillings which might contribute to the failure of endodontic treatment. To avoid this problem, a variety of sealers have been tested. The objective of this, in vitro, study was to evaluate the shear bond strength of four resin based sealers (AH plus, silver free AH26, RealSeal SE and Perma Evolution permanent root canal filling material) to dentin. Materials and Methods: Forty non-carious extracted lower premolars were used. The 2mm of the occlusal surfaces of teeth were sectioned, to expose the dentin surface. The exposed dentin surfaces of teeth were washed with 5ml of 2.5% NaOCl solution followed by 5ml of 17 % EDTA then rinsed by deionized water to remov

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Publication Date
Wed Jun 14 2023
Journal Name
Al-academy
The mechanisms of the actor's work between performance and directing style in the contemporary theater show (Western) as a model
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The actor has mechanisms that were applied in the performance، as it formed a style in the theatrical form (weird)، and the researcher deliberately studied these mechanisms and divided them into four chapters.

The researcher divided it into two sections، the first is the actor's performance requirements، and the second is the boring performance methods in the directors' theater، and then the researcher concluded the second chapter with the most important indicators.

As for the third chapter، the researcher determined the society of his research and the method of selecting the sample (strange) and analyzing the sample and concluded with the most important results of the sample analysis.

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Publication Date
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Apical Extrusion of Debris and Irrigants After using Different Irrigation Needles and Systems With Different Depth of Penetration (A Comparative Study)
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Publication Date
Sun Mar 06 2022
Journal Name
Al–bahith Al–a'alami
THE ETHICAL RESPONSIBILITY OF THE COMMUNICATOR IN PRESS INSTITUTIONS TO CONSOLIDATE THE VALUES OF TOLERANCE: A Study of the Communicator in the Newspapers (Al-Zaman, Al-Sabah, Al-Mada) For the period: 1/5/2020 to 1/10/2020
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This research deals with the role that the media can play in spreading awareness, culture and sound behavior among members of society, due to its ability to reach the largest number of individuals; its wide spread within society; and the moral responsibility of the media in consolidating the components of civil peace. The media works on forming intellectual convictions and behavioral attitudes by publishing opinions and ideas, introducing them to people's awareness and enhancing them in the practice of their daily lives, he was its media medium. Sociologists and psychologists confirm that the media. The significance of the research comes due to the broadening of violence and sectarian fighting; the absence of a culture of civil social pe

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Publication Date
Tue Apr 02 2019
Journal Name
Journal Of Environmental Health Science And Engineering
Adsorptive performance of a mixture of three nonliving algae classes for nickel remediation in synthesized wastewater
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Publication Date
Tue Apr 18 2023
Journal Name
Al–bahith Al–a'alami
Media policy and its impact on the level of objectivity in the Iraqi media : A study from the communicators’ point of view in the Iraqi medi outlets for the period from (1/5/2021 to 1/9/2021)
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The research aims to reveal the impact of media policy in Iraqi media outlets on the level of objectivity in these outlets. A study from the communicators’ point of view where the researcher used a survey method on the communicators in media outlets to reveal the extent of media policies knowledge as well as the pressures exerted by this policy on communicators in media outlets. It also reveals the extent of their commitment to objectivity, neutrality in dealing with information and the way used to transfer it.
The research sample included (179) respondents from communicators in a range of Media outlets such as (Press, Radio, and Television), The researcher was careful with the diversity of the sample, and

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Publication Date
Mon Feb 16 2026
Journal Name
Journal Of The College Of Basic Education
A comparative study between students of smokers and non-smokers in endurance antenna
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Subjects took physical fitness for health imposed on the area of research that have become an important and clear answer to the many problems resulting from the nature of dealing with modern life current actions that were needed to be hours of manual work has become accomplished by modern technology circumstance minutes, and mediated equipment And machinery. The lack of traffic rights and further burdens the intellectual and psychological pressures and the typical method of work has led to the identification of kinetic activity, thereby threatening public health in many ways stands at the forefront of these threats the problem of smoking, which causes many types of cancers, notably lung cancer. The most important reasons that led to This dr

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Publication Date
Fri Dec 14 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Evaluation of Diabetes Self-Management among Patients in Baghdad City: A Comparative Study
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Objective(s): To Evaluate Diabetes self –management among patients in Baghdad City and to compare
between these patients self-management relative to the type of the disease.
Methodology: A descriptive design was conducted in Baghdad city, started from November 16th 2017 to the
end of May 17 th 2018 in order to evaluate Diabetes self-management. Purposive (non-probability) sample,
which was consisted of (120) patients who were diagnosed with D.M. The sample is comprised of (60) patient
with diabetes type I and (60) patient with diabetes type II. It is consisted of (60) male and (60) female. A
questionnaire is constructed for the purpose of the study. It is composed of (42) items. Reliability and validity of
the ques

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Publication Date
Mon Jun 30 2025
Journal Name
Medical Journal Of Babylon
Assessment of Six Polymorphic Variants as Genetic Risks for Coronary Artery Disease: A Case–Control Study
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Abstract<sec> <title>Background:

Coronary artery disease (CAD) is the leading cause of death worldwide. Certain genetic polymorphisms play an important role in this multifactorial disease, being linked with increased risk of early onset CAD.

Objective:

To assess six genetic polymorphisms and clinical risk factors in relation to early onset nondiabetic Iraqi Arab CAD patients compared to controls.

Materials and Methods:

This case–contro

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