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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
Wed Nov 07 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Knowledge of Breastfeeding: A descriptive study among mothers in Kirkuk Governorate
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Aims: The present study aims at assessing mothers’ knowledge of breastfeeding in Kirkuk governorate,
besides determining the relationship between mothers’ knowledge and some of their demographic
attributes.
Methodolgy: A descriptive study was used the assessment approach and applied on mothers in Kirkuk
governorate from January 15th 2011 to July 25th
, 2011. Non-probability sampling a convenience sample of
(72) mothers, attending pediatric general hospital in Kirkuk governorate for following up the health status
of their children, was selected for the purpose of the study. A questionnaire was developed for the
purpose of the study. It was comprised of two parts; the first part includes the mothers' demographic

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Publication Date
Fri Mar 25 2022
Journal Name
Nasaq Journal
A Linguistic Study of Paronomasia (Al-Jinās ) in Arabic and English
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Paronomasia is a recognized rhetorical device by which poets could play with words that are similar or identical in form but different in meaning. The present study aims to identify paronomasia in Arabic and English. To achieve the aim of the study, a corpus of selected verses chosen from two famous figures in Arabic and English literatures and analyzed thoroughly. The analysis of data under investigation reveals that paronomasia is a crucial aid used by poets to portrait the real world as imaginative. It further shows that the concept of paronomasia in English is not the same as in Arabic. In English, there are echoes of the Arabic jinās, i.e., there are counterpart usages of similar devices, yet English rhetoricians have not defined or c

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Publication Date
Tue Dec 10 2019
Journal Name
London Metropolitan University
Speech intelligibility: a study of Iraqi EFL learners’ accented English
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MR Younus…, 2020 - Cited by 2

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Publication Date
Fri Dec 29 2017
Journal Name
Al-khwarizmi Engineering Journal
A Study Of Strengthening Circular Diaphragm By Ring-Shaped Concentric Ribs
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 This paper deals with the determination of stresses and deflections of clamped circular diaphragm strengthened by one or two ring-shaped concentric ribs, under uniform static and dynamic pressures. The simulation has been achieved by using the well-known engineering software finite element package MSC/NASTRAN

 As a design study, the effect of using a clamped ring, and the effect of using a ring-shaped rib on both surfaces of diaphragm instead of one, has been discussed in this work. To show the effectiveness of this study, results of this work have been compared with  published data [1].

In  the  conclusion,  the  authors underline  the  validity of  the&n

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Publication Date
Wed Sep 28 2022
Journal Name
Journal Of The College Of Education For Women
A Cognitive Linguistic Study of Battered Woman in Selected Iraqi Caricatures
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The present paper is a qualitative descriptive study. It aims to examine the macro-cultural schemata addressing the concept of violence against women in Iraq from a cognitive linguistic point of view. To meet this objective, a number of Iraqi social caricatures have been selected from two popular and active Iraqi caricaturists, Odeh Al-Fahdawi and Nasser Ibrahim. The selection and the analysis of data have been achieved following the validity and reliability procedures and the ethical considerations. To meet this objective, Sharifian’s Model (2011) of Cultural Schemata has been adopted in data analysis. The study has concluded that the macro-cultural schemata regarding the concept of violence in the selected panels reveals that violenc

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Publication Date
Mon Aug 25 2025
Journal Name
Al–bahith Al–a'alami
Organizational reputation: A descriptive study of concept development and measurement techniques
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The study aimed to monitor the concept of reputation in the previous literature, its relationship to mental image and identity, and to reveal recent trends in its measurement Techniques.

    The study relied on a descriptive approach using library survey and comparative analysis, and the study reached following conclusions:

     Despite the beginning of the first signs of reputation In the fifties of the last century, however, Defining and standardizing the concept with clear and specific dimensions began in the 1990s and the beginning of the third millennium. The concept of reputation refers to the stakeholders’ overall evaluation of organizations, which reflects their perceptions of

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Publication Date
Wed Nov 17 2021
Journal Name
7th International Conference On Multidisciplinary Sciences (7th Icomus)
A Critical Pragmatic Study of Sarcasms in American and British Interviews
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APDBN Rashid, 7th International Conference on Multidisciplinary Sciences (7th ICOMUS), 2021

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Publication Date
Thu Nov 01 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Life – Style of patients with peptic ulcer A case control study
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Abstract A descriptive (retrospective) (a case-control) study was carried out at Al-Karama Teaching Hospital, Baghdad Teaching Hospital and Surgical Specialties Hospital, and Gastro-Intestinal Tract and Liver (GIT) Hospital for the period of December 1st, 2001 To March 15th 2002. To identify aspects of life-style that may contribute to the occurrence of peptic ulcer (P.U)as risk factors. And to find out the relationship between the demographic characteristic of the group. Non-probability (Purposive) sample of (100) cases who were admitted to the endoscopy department who were later on diagnosed as having

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Publication Date
Fri Oct 01 2010
Journal Name
J Saudi Soc Dermatol Dermatol Surg
Outbreak of Thallium poisoning among Iraqi Patients: A case descriptive study
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KE Sharquie, GA Ibrahim, AA Noaimi, HK Hamudy, J Saudi Soc Dermatol Dermatol Surg, 2010 - Cited by 2

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Publication Date
Wed Jun 30 2010
Journal Name
Al-kindy College Medical Journal
A prospective study of colonoscopic examination at al-kindy teaching hospital
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Background: Fiber-optic endoscopy is an important
investigation of the large intestine, whether or not the
radiologist (barium enema) has discovered a lesion in
the bowel. Colonoscopy affords a unique opportunity
to direct visualization of entire colonic mucosa. At
the same time, the physician can obtain biopsy specimens, remove polyps, and decompress volvuli.
Most experienced endoscopists and well prepared
patients can reach the cecum in over 90% of patients.
If colonoscopy is properly performed, it has a low
risk of complications, such as perforation and bleeding.
Methods: A total of 70 consecutive patients admitted
to Endoscopy department at Al-Kindy Teaching hospital from September- 2008 to July-2009.

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