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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
Tue Nov 25 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Effects of three different types of intracoronal bleaching agents on shear bond strength of stainless steel and sapphire brackets bonded to endodontically treated teeth (An in vitro study)
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Background: evaluate the effects of three different intracoronal bleaching agents on the shear bond strengths (SBS) and failure site of stainless steel and monocrystalline (sapphire) orthodontic brackets bonded to endodontically treated teeth using light cured orthodontic adhesive in vitro. Materials and methods: Eighty extracted sound human upper first premolars were selected, endondontically treated and randomly divided equally (according to the type of the brackets used) into two main groups (n = 40 per group). Each main group were subdivided (according to the bleaching agent used) into four subgroups 10 teeth each; as following : control (un bleached) group, hydrogen peroxide group (Hp) 35%, carbamide peroxide group (CP) 37% group and s

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Publication Date
Tue Dec 05 2023
Journal Name
Baghdad Science Journal
Red Ginger's Anti-Anxiety Effect on BALB/c Strain Mice (Mus musculus) Pro-Inflammatory and Anti-Inflammatory Measurements as Anxiety Model
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There is a correlation between the occurrence of anxiety and the production of inflammatory mediators, and red ginger rhizome is a well-known herbal product with a high content of phenolic and flavonoid compounds that can be used as anti-inflammatories and antioxidants. The aim of study to evaluate the effect of red ginger as antianxiety in mice (Mus musculus) BALB/c strain by measuring levels of TNF-α, IL-6 and IL-10.  Anxiety model mice were carried out by giving treatment with the Forced Swimming Test (FST) for 7 days then assessed by carrying out the Elevated Plus Maze for Mice (EPM) test for one day. After the treatment, the anxiety mice model was made, followed by administration of red ginger ethanol extract therapy for 14 days.

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Publication Date
Thu Dec 31 2015
Journal Name
International Visible Conference On Educational Studies & Applied Linguistics 2016
A New Perspective About Masculinity and the Issue of Identity in Ernest Hemingway's The Old Man and The Sea and Michael Ondaatje's in The Skin of a lion
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A New Perspective About Masculinity and the Issue of Identity in Ernest Hemingway's The Old Man and The Sea and Michael Ondaatje's in The Skin of a lion

Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Social responsibility and its role in enhancing the quality of services: an analytical study of the views of a sample of employees in the Directorate of Electricity Distribution Nineveh / Center
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The current research aims to diagnose the role of social responsibility as a contributing factor in enhancing the quality of services provided by the public sector in Iraq, where the research sought to demonstrate the relationship and impact of social responsibility dimensions (economic, legal, moral, and human) on the sector Services related to the electric field in Nineveh governorate because of its importance and its direct relationship with the citizen especially after the end of military operations in the destruction of the electricity sector by a large percentage in the city of Mosul. Nineveh Electricity Distribution Directorate / Center was chosen as a research community including (administrators and staff) of the research

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Publication Date
Fri Mar 01 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Study the random walking of the ISX60 market index For the Iraq Stock Exchange
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This paper aimed to test random walking through the ISX60 market index for the ability to judge market efficiency at a weak level. The study used Serial Correlation Test, the Runs Test, the Variance Ratio Test, as well as the Rescaled Range Test.The population of the study represents of Iraq Stock Exchange. The study concluded accepting the hypothesis of the study that the returns of the ISX60 market index in the Iraqi market for securities does not follow the random walking in general and as a result the Iraq market for securities is inefficient within the weak level of efficiency and the study recommended need a supervisors work in the Iraqi market for securities to activate all means a which will work to communication with information

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Publication Date
Wed Jan 09 2019
Journal Name
Journal Of The College Of Education For Women
The Effect of Daniel's Model on the Acquisition of Concepts for the Arabic Language Curricula Among the Students of Department of Arabic Language in Colleges of Basic Education
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The current research aims to investigate the effect of a specimen of Daniel in the acquisition of concepts for the Arabic language curricula material to the students of the third phase of the Faculty of Basic Education Department of Arabic Language. The sample consists of (93) applications and a student of (47) students in the Division (A), which represents the experimental group which studied the use of a specimen of Daniel, and (46) students in the Division (B), which represents the control group, which studied the traditional way. The subject of unified two groups, which subjects the Arabic language curricula which includes six chapters.
The duration of the experiment is a full semester. The researchers also prepared a tool for mea

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Publication Date
Fri Jun 20 2025
Journal Name
Journal Of Kufa For Chemical Sciences
Synthesis, Characterization, Antimicrobial Activity of New Schiff Base Complexes and Thermodynamic Study for Adsorption of Pt(IV) Complex Using Bentonite
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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
High Commitment Management and their Impact in Organizational Excellence Afield Research for opinions a sample of managers in the company general Alfurat for chemical industries \Babylon
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In its theoretical framework, this study dealt with the subjects of high commitment management and organizational excellence, as the study came in response to the growing developments and changes in the fields of management. It includes an analysis of correlation and effect between high commitment management, which has been attracting a lot of attention recently due to the intensifying rivalry between organizations because of certain external factors like globalization and world markets liberation, and its effect in achieving organizational excellence.

The practical framework, on the other hand, dealt with the analysis of correlation and effect between the study's variables. The problem

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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Population Therapeutics And Clinical Pharmacology
Accuracy of Office Hysteroscopy in Diagnosis of Endometrial Pathologies Compared to Ultrasound and Histopathology in Baghdad Teaching Hospital
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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Population Therapeutics And Clinical Pharmacology
Accuracy of Office Hysteroscopy in Diagnosis of Endometrial Pathologies Compared to Ultrasound and Histopathology in Baghdad Teaching Hospital
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Background: Menstrual problems with all manifestations ranging from life-threatening bleeding to amen- orrhea are considered patterns of abnormal uterine bleeding (AUB), which is until now a popular reason for referral to the gynaecologic clinic and requires a special diagnostic tool. Objective: To assess the accuracy of hysteroscopy in diagnosing endometrial pathologies and to compare it with sonographic and histopathologic reports. Patients and Methods: A prospective study conducted in the Baghdad Teaching Hospital on 60 Iraqi females having varying complaints from abnormal uterine bleeding in pre- and post-menopausal women, infertility, and chronic pelvic pain with normal or abnormal ultrasound findings. Office hysteroscopy was done and

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