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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 Jan 01 2024
Journal Name
Journal Of Medicine And Life
Antimicrobial photodynamic therapy using a low-power 650 nm laser to inhibit oral Candida albicans activity: an in vitro study
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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
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
The women at Al-Sakhaawi Book "A;-Dhau Al-Lami", Study in the social life
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In our previous research , we study the method of women by ( al – sakhaawi " died 902
ah/1496a.c"book witch called ( al- dhau, al-lami) .
So in this paper , we will discuss the social life of women in the mamluk period through the
same book ,especially when the sakhaawi devoted a full part for women in the same book
called it (mhagam ,al –nessa)wich it translations a large number of women like wives
,daughters ,sisters ,and maids of mamluk sultans ,so that make my able to know a lot about
the social life of woman which we study it like a social aspects of women, here wealth,
business, professions ,and in the last we study the habits of them marriage .

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Publication Date
Sun Mar 17 2019
Journal Name
Baghdad Science Journal
Study of Aerodynamic Surface Roughness for Baghdad City Using Signal-Level Measurements
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Roughness length is one of the key variables in micrometeorological studies and environmental studies in regards to describing development of cities and urban environments. By utilizing the three dimensions ultrasonic anemometer installed at Mustansiriyah university, we determined the rate of the height of the rough elements (trees, buildings and bridges) to the surrounding area of the university for a radius of 1 km. After this, we calculated the zero-plane displacement length of eight sections and calculated the length of surface roughness. The results proved that the ranges of the variables above are ZH (9.2-13.8) m, Zd (4.3-8.1) m and Zo (0.24-0.48) m.

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Publication Date
Wed Mar 01 2023
Journal Name
Baghdad Science Journal
Pharmacokinetic Consideration to Formulate Sustained Release Drugs: Understanding the Controlled Drug Diffusion through the Body Compartment of the Systemic Circulation and Tissue Medium-A Caputo Model
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The aim of this study is to provide an overview of various models to study drug diffusion for a sustained period into and within the human body. Emphasized the mathematical compartment models using fractional derivative (Caputo model) approach to investigate the change in sustained drug concentration in different compartments of the human body system through the oral route or the intravenous route. Law of mass action, first-order kinetics, and Fick's perfusion principle were used to develop mathematical compartment models representing sustained drug diffusion throughout the human body. To adequately predict the sustained drug diffusion into various compartments of the human body, consider fractional derivative (Caputo model) to investiga

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Publication Date
Sat Oct 20 2018
Journal Name
Journal Of Economics And Administrative Sciences
Fluctuations of global crude oil prices and their effect on inflation and economic growth in Iraq " A standard study for the period 1988– 2015
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Abstract

That Iraq's dependence on the revenues of the oil product in financing its development programs and growth rates , Making the economy affected by external forces represented by fluctuations in crude oil prices in the global market, Which is directly reflected on the performance and efficiency of the Iraqi economy.

The study adopted its objectives to analyze the time series for the period (1988 - 2015) through the use of standard and statistical methods, Four standard models were estimated to reach those targets, Where the results of the stability test showed instability of most variables at their original level, But to achieve stability when taking the first differences, While the result

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Publication Date
Wed Oct 02 2024
Journal Name
International Development Planning Review
THE EFFECT OF EXERCISES USING A MINI SQUASH COURT ON IMPROVING SOME MOTOR ABILITIES AND LEARNING SOME BASIC SKILLS FOR PLAYERS AGED 10-12 YEARS
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Publication Date
Wed Oct 02 2024
Journal Name
International Development Planning Review
THE EFFECT OF EXERCISES USING A MINI SQUASH COURT ON IMPROVING SOME MOTOR ABILITIES AND LEARNING SOME BASIC SKILLS FOR PLAYERS AGED 10-12 YEARS
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Publication Date
Thu Jan 06 2022
Journal Name
Chemical Papers
A solvent collection technique using dispersive liquid–liquid microextraction coupled with spectrophotometry for the trace determination of folic acid in pure, dosage forms and flaxseed
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A simple, rapid and environmentally friendly dispersive liquid–liquid microextraction method-based spectrophotometric method for the trace determination of folic acid has been developed. The proposed method is based on the formation of a deep yellow product via reaction of folic acid and 1,2-naphthoquine-4-sulfonate at pH = 9. The formed complex was extracted using a mixture of chloroform and ethanol. Then, the tiny organic droplets were measured at λ = 520 nm. At the optimum conditions, linearity was ranged from 0.05 to 1.5 μg/mL for the standard and samples, with a linear correlation coefficient of 0.9996. The detection limits were 0.02, 0.027, 0.03, 0.02 and 0.04 μg/mL for standard, tablet (5 mg), tablet (1 mg), syrup and fl

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