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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 Feb 12 2019
Journal Name
Iraqi Journal Of Physics
A Study of the generation of laser soliton from spontaneous emission by ring cavity with carbon nanotube
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We demonstrate a behavior of laser pulse grows through fiber laser inside and output cavity with a soliton fiber laser based on the multi-wall carbon nanotube saturable absorber (SA), we investigate the effects of a saturable absorber parameter on the mode-locking of a realistic Erbium fiber ring laser. Generalized nonlinear Schrodinger equation including the nonlinear effects as gain dispersion, second anomalous group velocity dispersion (GVD), self phase modulation (SPM), and two photon absorption used to describe pulse evolution. An analytical method has been used to understand and to quantify the role of the SA parameter on the propagation dynamics of pulse laser. We compute the chirp, power, width and phase of the soliton for range

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Publication Date
Sun Apr 30 2023
Journal Name
International Journal Of Design & Nature And Ecodynamics
Evaluation of the Minimum Instream Flow: A Case Study of Shatt-Al Hillah River in Babylon Governorate
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Publication Date
Tue Jun 30 2015
Journal Name
Al-kindy College Medical Journal
A study of the effect of smoking on pulmonary function tests in AL - Kindy teaching hospital, Baghdad
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ABSTRACTBackground: In Iraq smoking is a common habit in both the urban and rural areas. There are many respiratory diseases like chronic bronchitis, bronchial carcinoma and emphysema which are related to chronic tobacco smoking.Objectives: To study the effect of tobacco smoking on the respiratory system, to establish a correlation between chronic tobacco smoking and its effects on the parameters which were studied and to create awareness in tobacco smokers about the effects of tobacco on their healthMethod: In this study 100 male subjects, 50 chronic smokers and 50 non- smokers were assessed for their pulmonary function tests by using a computerized spirometer.Results: Almost all their respiratory parameters were significantly reduced.

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Publication Date
Wed Jun 03 2015
Journal Name
Al-kindy College Medical Journal
Aneurysmal bone cyst of the lateral end of clavicle in a twelfth year old girl Case study
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Introduction: An aneurysmal bone cyst are enigmatic lesion of unknown cause and presentation and are difficult to distinguish from other lesions, it is a benign, but expansible tumor like lesion that generally occurs in the long bones. An aneurysmal bone cyst arising from the flat bone like clavicle is rare . Case presentation: We report a 12-year-old girl child with an aneurysmal bone cyst of the lateral third of left clavicle treated with enblock resection. The pathologic findings confirmed the diagnosis of aneurysmal bone cyst. The patient has been followed up for one year with no evidence of recurrence . Conclusion: En bloc resection can be curative and provide good results for this rare type of clavicle tumour.

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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Stomatology
Preferences of treatments and materials used in the management of exposed pulps: a web-based questionnaire study
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Publication Date
Wed Sep 30 2020
Journal Name
College Of Islamic Sciences
Arabization and its contemporary applications A jurisprudential study of the provisions and certifications of Arabization and migration
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The place in which the person lives and his geographical and social environment have a great impact on building his personality, belief and culture, Islam has alerted the importance of the Muslim to make sure to choose the appropriate place in which he resides and dwells in that it is compatible with his religion and belief in order to ensure communication with Islamic knowledge in a way that enhances his belief Arabization occurs when a person makes himself an Arab by living the life of the Bedouins, and creates the morals of the Bedouins from the inhabitants of the Badia with its harshness, cruelty, ignorance and lack of understanding in religion and far from the sources of knowledge of Islamic knowledge. Blasphemy and polytheism, and

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Publication Date
Tue Jun 30 2015
Journal Name
Al-kindy College Medical Journal
Aneurysmal bone cyst of the lateral end of clavicle in a twelfth year old girl Case study
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Introduction: An aneurysmal bone cyst are enigmatic lesionof unknown cause and presentation and are difficult todistinguish from other lesions, it is a benign, but expansibletumor like lesion that generally occurs in the long bones. Ananeurysmal bone cyst arising from the flat bone like clavicleis rare .Case presentation: We report a 12-year-old girl child with ananeurysmal bone cyst of the lateral third of left clavicletreated with enblock resection. The pathologic findingsconfirmed the diagnosis of aneurysmal bone cyst. Thepatient has been followed up for one year with no evidenceof recurrence .Conclusion: En bloc resection can be curative and provide good results for this rare type of clavicle tumour.

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Publication Date
Thu Jun 01 2023
Journal Name
Magazine Aldhakwat Albedh
The methodology of Ibn Mamati (d. 606 AH) in his book Laws of Diwans - A Civilizational Study
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The book The Laws of Duwan of Mamati's Son (T, 606 E) His approach to his narratives is a topic of historical and civilized importance. The Fatimid Age of the People of Jehovah has expanded its influence and authority, including ministers, writers, doughnuts and foreshores. One of the Christian families that shined in the late Fatmi era was "Mamati", who lived in "Assiut" from Upper Egypt, then moved to Cairo, and enrolled in the service of the Fatimids, where their sons held important positions in State offices.Ibn Mamati became in charge of the Army Office and then added to it the Finance Office, which became the most important downs in Egypt. Through his work in the Duwan Law Books, this book was a living record of the Dawawans in the Ay

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Publication Date
Mon Oct 01 2018
Journal Name
Al–bahith Al–a'alami
International News Agencies Treatment of the Great Return Marches A Case Study of Agence France Presse “AFP”
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This study examines Agence France Presse’s (AFP) media treatment of the Great Return Marches in order to identify its contents, the issues it gave attention to, its sources, attitude, techniques, objectives, the journalistic forms used in covering events and the typographic elements used to highlight them.

This descriptive study employed the survey methodology through the use of content analysis method, and the methodology of mutual relations through the use of the case study method. The data was collected by means of a content analysis form. The study was based on the Agenda Setting Theory in the analysis of the study results.
The study sample included (116) news texts from AFP collected during the period from 20/3/2018 to

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Publication Date
Tue Aug 26 2025
Journal Name
Journal Of Physical Education
Analytical Study of Goalkeeper Positioning Using MH System for Free Kick in Soccer
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