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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
Mon Jun 19 2023
Journal Name
Journal Of Engineering
Study of Some Mechanical Properties for a Polymer Material Reinforcement with Chip or Powder Copper
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In this paper, chip and powder copper are used as reinforcing phase in polyester matrix to form composites. Mechanical properties such as flexural strength and impact test of polymer reinforcement copper (powder and chip) were done, the maximum flexural strength for the polymer reinforcement with copper (powder and chip) are (85.13 Mpa) and (50.08 Mpa) respectively was obtained, while the maximum observation energy of the impact test for the polymer reinforcement with copper (powder and chip) are (0.85 J) and (0.4 J) respectively  

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Publication Date
Thu May 23 2019
Journal Name
The International Journal Of Artificial Organs
Real-time classification of shoulder girdle motions for multifunctional prosthetic hand control: A preliminary study
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In every country in the world, there are a number of amputees who have been exposed to some accidents that led to the loss of their upper limbs. The aim of this study is to suggest a system for real-time classification of five classes of shoulder girdle motions for high-level upper limb amputees using a pattern recognition system. In the suggested system, the wavelet transform was utilized for feature extraction, and the extreme learning machine was used as a classifier. The system was tested on four intact-limbed subjects and one amputee, with eight channels involving five electromyography channels and three-axis accelerometer sensor. The study shows that the suggested pattern recognition system has the ability to classify the sho

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Publication Date
Tue Jan 27 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Management of Independent Middle Mesial Canal in Mandibular First Molar Using Cone Beam Computed Tomography Imaging as an Adjunct – A Case Report
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The primary objective of root canal therapy is adequate biomechanical preparation of root canal system followed by 3D obturation.in clinics we are encountered with several anatomical variations, which we need to manage efficiently. One of the major factors responsible for failure of root canal therapy is missed canals. Recent technological advances have given the clinician opportunity to identify anatomical variations and treat them to satisfaction.

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Publication Date
Sun Jan 20 2019
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Synthesis, Antibacterial and Antifungal Activities for Novel Derivatives of 2,2'-(((1-benzylbenzoimidazol-2-yl)methyl)azanediyl)bis(ethan-1-ol)
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The compound 2,2'-(((1H-benzo(d)imidazol-2-yl)methyl)azanediyl)bis(ethan-1-ol) was reacted with benzyl bromide to afford compound (1) which used as row material to prepare a series of compounds through condensation reaction, the starting compound were reacted with tosyl chloride to protect the OH group  to afford compound 2, then reacted benzyl bromide to produce compound (2), then the compound (2) treated with three compounds ( 2-mercaptobenzthiazole, 2-mercaptobenimidazol and 2-chloromethyl benzimidazole) to form compounds 3a,b, 4a,b and 5a,b respectively. In the another step the click reaction of compound 2,2'-(((1H-benzo(d)imidazol-2-yl)methyl)azanediyl)bis(ethan-1-ol) with Propargyl bromide produce compound  6  which reacted

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Publication Date
Thu Aug 01 2019
Journal Name
Nanomedicine: Nanotechnology, Biology And Medicine
Listeria innocua Dps as a nanoplatform for bioluminescence based photodynamic therapy utilizing Gaussia princeps luciferase and zinc protoporphyrin IX
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Publication Date
Sun Sep 06 2009
Journal Name
Baghdad Science Journal
A Study of the Nutritional Behavior and Body Mass Indexes for Students of Age (17-25) Years In Baghdad, Iraq.
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The aim of this study was to assess the nutritional status for samples at the age of 17-15 years. These samples were taken from secondary schools and universities in Baghdad area, 123 of them were male and 261 were female. Data on weight, height and body mass index (BMI) were determined in each individual. Smaller sample of 215 individuals (male and female) from the original sample was taken in order to record their nutritional behavior and daily food intake during the 24 hours prior to the visit through personal meeting using special questionnaire. The results showed that the weight and the height were within the range of the people of neighboring Arab countries, who are in the same age. Beside 44.4- 55.95% of these samples were within t

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Publication Date
Sat Mar 30 2024
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Optimization of Separator Size and Operating Pressure for Three-phase Separators in the West Qurna1 Oil Field
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An optimization study was conducted to determine the optimal operating pressure for the oil and gas separation vessels in the West Qurna 1 oil field. The ASPEN HYSYS software was employed as an effective tool to analyze the optimal pressure for the second and third-stage separators while maintaining a constant operating pressure for the first stage. The analysis involved 10 cases for each separation stage, revealing that the operating pressure of 3.0 Kg/cm2 and 0.7 Kg/cm2 for the second and third stages, respectively, yielded the optimum oil recovery to the flow tank. These pressure set points were selected based on serval factors including API gravity, oil formation volume factor, and gas-oil ratio from the flow tank.    To impro

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Publication Date
Sun Jan 01 2023
Journal Name
Brazilian Dental Science
Wound healing effect of a one-week Aloe Vera mouthwash: a pilot study
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Publication Date
Wed Jan 01 2020
Journal Name
Transplantation Proceedings
Outcomes of SGLT2 Inhibitors Use in Diabetic Renal Transplant Patients
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Publication Date
Wed Mar 23 2022
Journal Name
Journal Of Educational And Psychological Researches
The level of evaluation of the educational counselors ’performance as a predictor of their level of satisfaction with their evaluation
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The current research aims to reveal the level of satisfaction of the mentors with the evaluation of their performance according to gender (male - female) and to formulate the predictive equation for the level of performance (dependent variable) from knowing the level of satisfaction with the evaluation (independent variable). (16 paragraphs) contains alternatives to the answer that measures the level of satisfaction (weak, medium, and high) (1,2,3), that is, with a hypothetical average of (32). It consisted of 100 educational counselors consisting of 45 males and 55 females, the results of the research concluded that the level of satisfaction with performance is below the mean when compared with the hypothetical average of the scale of s

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