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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 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
Sat Oct 03 2020
Journal Name
International Journal Of Pharmaceutical Research
Serum Afamin As A Novel Biomarker for NonAlcoholic Fatty Liver Disease as A Complication of Hypothyroidism in Iraqi Patients.
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Afamin, which is a human plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome. Afamin concentration have been proposed to have a significant role as a predictor of metabolic disorders. Since NAFLD is associated with metabolic risk factors, e.g., dyslipidemia, insulin resistance and visceral obesity, it is considered as the hepatic manifestation of the metabolic syndrome. The objective of this study is to determine Afamin levels in hypothyroid patients with and without fatty liver disease and compare the results with controls. Also to study the relationship of Afamin level with the Anthropometric and Clinical Features (Age, Gender, BMI and Duration of Hypothyroidism) , Serum

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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
Wed Aug 06 2025
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
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
The Romantic Nightingale between Coleridge’s Divergence and Keats’ Adherence: A comparative Study between Coleridge’s ‘The Nightingale’ and Keats’ ‘Ode to a Nightingale’
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‘Ode to a Nightingale’(1819) is a typical poem of a Romantic poet like John Keats, but
‘The Nightingale’(1798) is an uncharacteristic poem of a Romantic poet like Coleridge.
The paper proposes a comparison between Coleridge’s ‘The Nightingale’ and Keats’
‘Ode to a Nightingale’.Coleridge’s poem diverges from the Romantic norm; it carries some
characteristics new to Romantic poetry like the realistic and objective portrayals of nature and
the nightingale, while Keats’ poem adhere to the characteristics of Romantic poetry; it
portrays nature and the nightingale subjectively and unrealistically. Coleridge’s poem is very
much influenced by the scientific approaches to environment, and natural his

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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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Publication Date
Fri Oct 28 2022
Journal Name
Political Sciences Journal
Applications of contemporary feminist theory and its role in international relations (Singapore as a Model)
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Since the emergence of the science of international relations as an independent academic scientific field,  various theories and trends have appeared and have tried to understand and explain the international reality and give a clear picture of what is happening within the international system of interactions and influences and the search for tools for stability and peace in international relations. Among these theories is the feminist theory, which is a new intellectual trend on the level of international relations theories,  which tried to give an explanation of what is happening in world politics and in international relations in particular. The main issue that feminist theory is concerned with is the lack of women’s subordination

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Publication Date
Fri Dec 01 2017
Journal Name
British Journal Of Oral And Maxillofacial Surgery
A novel approach for the three-dimensional evaluation of facial asymmetry of unilateral cleft lip and palate patients (UCLP)
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Publication Date
Wed Aug 06 2025
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
Sun Oct 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Mackenzie role model dimensions in the quality of service, "a Prospective study of the views of a sample of Iraqi banks managers
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The organizational integration forms a necessity according to McKinsey model, especially for service organizations. In the context of various service sector developments, importance adoption of compact mechanisms by these organizations to upgrade their services has increased and senior management must be more aware of environmental, competitive and developmental requirements. It gets more important when it shows in an organization seeking at excellence of making services within its policies and strategies. Subject organizational integration dimensions (strategy, structure, systems, style, staff, shared values, and skills) are effective components in directing behaviors of employees and organization. This motivated both researcher

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