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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 Dec 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Correlation between Periodontal Health Status and Salivary Matrix Metalloproteinase-9 Levels in Smoker and Non-Smoker Chronic Periodontitis Patients (A Comparative Study)
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Background: Periodontal diseases are inflammatory diseases affecting the supporting tissues of the teeth. One of the leading environmental factors that are closely related not only to the risk but also to the prognosis of periodontitis is smoking. This study aimed to evaluate the influence of smoking on periodontal health status and to measure the levels of matrix metalloproteinase-9 in smokers and nonsmokers chronic periodontitis patients, also it aimed to test the correlation between the levels of matrix metalloproteinase-9 and the clinical periodontal parameters. Materials and Methods: Five milliliters samples of un-stimulated whole saliva and full-mouth clinical periodontal recordings (plaque index, gingival index, bleeding on probing,

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Evaluate the implementation of the investment plan projects A study on the field of the plan projects for the period 2013-2016
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The main problem of this research is the delay of implementation of the investment plan projects for the period (2013-2016) and the weakness of the staff ability in the ministries and they don’t have the sufficient experience to carry out the implementation process.

Therefore, the research aims to evaluate the implementation of programs and projects of the investment plan in a manner consistent with the objectives set for them without any wasteful of efforts, time and money. And then identify the problems and obstacles to determine the deviations of the implementation of the specific for each sector according to the criteria of evaluation and the form of cost, quality, time and implementation.<

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Publication Date
Wed Jan 26 2022
Journal Name
Iraqi Journal Of Science
Potentiometric Determination of Mebeverine Hydrochloride Using Imprinted Molecular Polymer in PVC Matrix Membrane‏
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Publication Date
Mon Jun 23 2025
Journal Name
Journal Of Craniofacial Surgery
Gender Determination in Forensic Dentistry Using Bonwill’s Triangle Measurements From CBCT Scans: A Study on the Iraqi Population
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Background:

The purpose of this study is to illuminate the role of CBCT in forensic dentistry through variations of mandibular measurements of Bonwill’s triangles in gender determination among the Iraqi population.

Materials and methods:

In this retrospective study 70 CBCT scans were analyzed to measure the Bonwill’s triangle, 35 for males and 35 for females aged between 20 and 50 years, all data were collected at the oral and maxillofacial radiology department in Ghazi AL-Hariri hospital for 3 months, and the data were obtained using a Kavo CBCT device (3D On De

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Publication Date
Sat Jan 25 2020
Journal Name
Indian Journal Of Forensic Medicine &amp; Toxicology
A Comparative Evaluation of Gutta-Percha and Sealer Removal of Rotary Niti File Retreatment Systems
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Forty lower premolars with single root canals prepared with ProtaperNext files to size 25, and obturated with GP/sealer using lateral compaction. Teeth divided randomly into four groups (group n=10). Protaper universal retreatment kit (PUR), D-Race desobturation files (DRD), R-Endo retreatment kit (RE) and Hedstrom (H) files (control) were used to remove GP/sealer in each group. Removal effectiveness assessed by measuring the GP /sealer remnants in the roots after sectioning them into two halves. Stereomicroscope with a digital camera used to capture digital images. Images processed by ImageJ software to measure the percentage of GP/sealer remnants surface area in total, coronal, middle and apical areas of the canal. In the coronal area,

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Publication Date
Thu Jan 02 2020
Journal Name
Indian Journal Of Forensic Medicine &amp; Toxicology
A Comparative Evaluation of Gutta-Percha and Sealer Removal of Rotary Niti File Retreatment Systems
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Publication Date
Fri Jul 21 2023
Journal Name
Journal Of Engineering
SIMULATION OF OPTIMAL SPEED CONTROL FOR A DC MOTOR USING LINEAR QUADRATIC REGULATOR (LQR)
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This paper describes DC motor speed control based on optimal Linear Quadratic Regulator (LQR) technique. Controller's objective is to maintain the speed of rotation of the motor shaft with a particular step response.The controller is modeled in MATLAB environment, the simulation results show that the proposed controller gives better performance and less settling time when compared with the traditional PID controller.

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
(Estimation and Analysis of the Cobb-Duglas Production Function for the Rail Transport Sector in Iraq for the Period 1990-2016 using the ARDL Model)
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Abstract:

Since the railway transport sector is very important in many countries of the world, we have tried through this research to study the production function of this sector and to indicate the level of productivity under which it operates.

It was found through the estimation and analysis of the production function Kub - Duglas that the railway transport sector in Iraq suffers from a decline in the level of productivity, which was reflected in the deterioration of the level of services provided for the transport of passengers and goods. This led to the loss of the sector of importance in supporting the national economy and the reluctance of most passengers an

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Publication Date
Sun Sep 27 2020
Journal Name
Iraqi National Journal Of Nursing Specialties
Evaluation of Health Promotion Program for the Prevention of Epidemics at Primary Health Care Centers in Baghdad City: Comparative Study
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Objective(s): To evaluate and compare between Health Promotion Program for the Prevention of Epidemics at Primary Health Care Centers in Baghdad City.

Methodology: A descriptive study, using the evaluation and comparative approaches, is conducted to evaluate health promotion program for the prevention of epidemics at primary health care centers in baghdad city from October 15th  2019 through March 1st 2020. A purposive, non-probability, sample of (42) health promotion unit officers were recruited from the same number of primary health care centers which were divided into (14) main, (14) sub and (14) family medicine primary health care centers i

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Publication Date
Mon Sep 19 2022
Journal Name
Gynecology And Obstetrics Case Report
A Case Report of Intrauterine Fetal Death with Three Loops of Umbilical Cord around Neck, Keratin Hair Treatment during Pregnancy Could be the Cause
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