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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
Thu Dec 01 2022
Journal Name
Baghdad Science Journal
Enhancement Ear-based Biometric System Using a Modified AdaBoost Method
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          The primary objective of this paper is to improve a biometric authentication and classification model using the ear as a distinct part of the face since it is unchanged with time and unaffected by facial expressions. The proposed model is a new scenario for enhancing ear recognition accuracy via modifying the AdaBoost algorithm to optimize adaptive learning. To overcome the limitation of image illumination, occlusion, and problems of image registration, the Scale-invariant feature transform technique was used to extract features. Various consecutive phases were used to improve classification accuracy. These phases are image acquisition, preprocessing, filtering, smoothing, and feature extraction. To assess the proposed

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Publication Date
Wed Jun 11 2003
Journal Name
Iraqi Journal Of Laser
Microdrop Size Measurement in a Mixing Unit Using Laser Technique
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One of the troublesome duties in chemical industrial units is determining the instantaneous drop size distribution, which is created between two immiscible liquids within such units. In this work a complete system for measuring instantaneous droplet size is constructed. It consists of laser detection system (1mW He-Ne laser), drop generation system (turbine mixer unit), and microphotography system. Two immiscible liquids, water and kerosene were mixed together with different low volume fractions (0.0025, 0.02) of kerosene (as a dispersed phase) in water (as a continuous phase). The experiments were carried out at different rotational speed (1180- 2090 r.p.m) of the turbine mixer. The Sauter mean diameter of the drops was determined by la

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Publication Date
Wed Jun 29 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Measuring Dyes Concentration Using a Low-Cost Visible-Light Spectrophotometer
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   A low-cost, RGB LED-based visible-light spectrophotometer was designed to measure dyes concentration. Dyes are widely used as indicators or coloring agents in different applications and knowing their concentration is an essential part for many studies. The proposed spectrophotometer provides many functionalities that clones the traditional expensive spectrophotometers for a budged price under $50. It was aimed to provide a versatile tool for instructors and educators to teach their students the fundamental concepts behind spectrophotometry. Malachite green, methyl red, and methyl orange dyes were chosen to be good samples to show the integrity of the proposed spectrophotometer in terms of accuracy, repeatability, and sensitivity as

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Publication Date
Fri May 11 2018
Journal Name
Biomedical And Pharmacology Journal
Molecular and Phylogenetic Analysis of Human Papillomavirus Using L1 Gene in Oral Squamous Cell Carcinoma Patients in Baghdad, Iraq
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Oral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral mucosa. Human papillomavirus (HPV) virus cause a broad scope of diseases from benign to invasive tumors, types 16 and 18 classified as carcinogenic to humans. This study aimed to provide the first molecular characterization of HPV types in Iraq. Thirty-five unstimulated whole saliva samples were collected from histopathologically confirmed patients with oral cancer were enrolled in this study. Genomic DNA was extracted from exfoliating cells to amplify HPV-DNA using HPV-L1 gene sequence primers by polymerase chain reaction method (PCR), the viral genotyping was performed using direct sequencing method. HPV genotypes identified were deposited in Gen

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Publication Date
Fri May 11 2018
Journal Name
Biomedical And Pharmacology Journal
Molecular and Phylogenetic Analysis of Human Papillomavirus Using L1 Gene in Oral Squamous Cell Carcinoma Patients in Baghdad, Iraq
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Oral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral mucosa. Human papillomavirus (HPV) virus cause a broad scope of diseases from benign to invasive tumors, types 16 and 18 classified as carcinogenic to humans. This study aimed to provide the first molecular characterization of HPV types in Iraq. Thirty-five unstimulated whole saliva samples were collected from histopathologically confirmed patients with oral cancer were enrolled in this study. Genomic DNA was extracted from exfoliating cells to amplify HPV-DNA using HPV-L1 gene sequence primers by polymerase chain reaction method (PCR), the viral genotyping was performed using direct sequencing method. HPV genotypes identified were deposited in Gen

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Publication Date
Sun Aug 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Assessment of Oral Health in Hypertensive Patients Treated with HMG-CoA Reductase Inhibitors (Statins)
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Background: Hypertension is a chronic medical condition in which the blood pressure in the arteries is elevated, it's classified as either primary (essential) hypertension or secondary hypertension, and it increases the risk of ischemic heart disease, peripheral vascular disease and other cardiovascular diseases. Several classes of medications collectively referred to as antihypertensive drugs like beta blockers, calcium channel blockers, angiotensin converting enzyme (ACE) inhibitors, angiotensin receptor blockers, renin inhibitors and statins (HMG-CoA) reductase inhibitor. Statin medication may have some beneficial effects when subjects have dental plaque or signs of periodontitis as gingival bleeding. The purpose of this study were to as

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Publication Date
Mon Mar 15 2010
Journal Name
Journal Of Baghdad College Of Dentistry
Ear lobes as facial landmarks for determining the occlusal plane
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Background: Difficulties arise when attempting to imagine the interpupillary line and comparing it with the Fox plane guide and not more difficult than holding any instrument over the movable pupils just to demonstrate the interpupillary line. The aim of this study was to introduce ear lobes as alternative landmarks for the interpupillary line during orientation of the occlusal plane. Also, the other aim was to compare the ear lobes with the pupils of the eyes to verify that they were indifferent as anatomical landmarks. Materials & methods: The alternative landmarks, ear lobes, were presented and the method for orienting the occlusal plane with these landmarks was introduced. Digital pictures of 30 subjects, who participated in the study,

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Publication Date
Sat Apr 01 2017
Journal Name
2017 International Conference On Environmental Impacts Of The Oil And Gas Industries: Kurdistan Region Of Iraq As A Case Study (eiogi)
Inverse fluidized bed for chromium ions removal from wastewater and produced water using peanut shells as adsorbent
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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Settling Accounts of tax According to the unified Tax A Suggested Mechanism for: Application in the general Commission for Taxes
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Consistent "with the thought of tax talk is unified tax natural evolution for him, as the application leads to the inclusion of tax all branches of income and its sources and through truncated part of this entry through the application of price ascending it, it means the procedures of tax reform. Taxes on total income characterized by giving a clear picture of the total income of the taxpayer and its financial situation and its burden family which allows granting exemptions, downloads, and application of prices that fit this case. This requires reconsideration of the structure of the tax system in force and the transition from a system specific taxes to the tax system on the total income of the integration of income from the rental of re

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of The College Of Languages (jcl)
Sound Assimilation in English and Arabic: a Contrastive Study
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      This piece of research deals with assimilation as one of the phonological processes in the language. It is a trial to give more attention to this important process in English language with deep explanation to its counterpart in Arabic. in addition, this study sheds light on the points of similarities and differences concerning this process in the two languages. Assimilation in English means two sounds are involved, and one becomes more like the other.

     The assimilating phoneme picks up one or more of the features of another nearby phoneme. The English phoneme /n/ has t

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