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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 Feb 01 2024
Journal Name
Baghdad Science Journal
Molecular study of the relationship of gene expression of some genes with the temperature variation of bacterial growth
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Pseudomonas aeruginosa is an opportunistic pathogen responsible for serious infections. At least three different exopolysaccharides, alginate, polysaccharide synthesis locus (Psl), and pellicle exopolysaccharide (Pel) make up the biofilm matrix in P. aeruginosa . The effect of temperature on the biofilm formation and gene expression was examined by microtiter plate and real-time quantitative polymerase chain reaction (qRT-PCR). To be able to determine the effect of temperature on biofilm formation and gene expression of P. aeruginosa, 303 clinical and environmental samples were collected. Pseudomonas aeruginosa was isolated from 61 (20.1%) and 48 (15.8%) of the clinical and e

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Publication Date
Mon Feb 25 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Impact of Using the Information Technology on The Audit Profession: A Study of the Sample of Auditor Viewpoints in Selected Arab Countries
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This study aims to clarify areas of using information technology in accounting and its impact on the profession of auditors by reviewing the concept, types, areas and the importance of information technology and its implications on the audit profession as well as to clarify the extent of contribution of information technology in  developing of procedures of the audit profession and what its requirement, also this study aims to enhance the theoretical side by identifying the views of a sample of auditors in  Arab countries selected (Iraq, Syria, Jordan), for the extent of using of information technology in their work and level of their perception for the importance of that

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Publication Date
Thu Nov 20 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A study to compare the efficiency of different instrumentation systems for cleaning oval-shaped root canals (An in vitro study)
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Background: Proper cleaning and shaping of the whole root canal space have been recognized as a real challenge, particularly in oval-shaped canals.This in vitro study was conducted to evaluate and compare the efficiency of different instrumentation systems in removing of dentin debris at three thirds of oval-shaped root canals and to compare the percentage of remaining dentin debris among the three thirds for each instrumentation system. Materials and methods: Fifty freshly extracted human mandibular molars with single straight oval-shaped distal root canals were randomly divided into five groups of ten teeth each. Group One: instrumentation with ProTaper Universal hand instruments, Group Two: instrumentation with ProTaper Universal rotary

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Publication Date
Thu Nov 20 2025
Journal Name
Journal Mustansiriyah Of Sports Science
The Effect of Ocular Reflex Exercises Using a Proposed Device on Eyes - Hands Coordination for Junior Boxers
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Publication Date
Fri Mar 01 2024
Journal Name
Journal Of Applied Spectroscopy
Spectrophotometric Method for Determination of Cu(II) Using a New Schiff Base Ligand
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The Cu(II) was found using a quick and uncomplicated procedure that involved reacting it with a freshly synthesized ligand to create an orange complex that had an absorbance peak of 481.5 nm in an acidic solution. The best conditions for the formation of the complex were studied from the concentration of the ligand, medium, the eff ect of the addition sequence, the eff ect of temperature, and the time of complex formation. The results obtained are scatter plot extending from 0.1–9 ppm and a linear range from 0.1–7 ppm. Relative standard deviation (RSD%) for n = 8 is less than 0.5, recovery % (R%) within acceptable values, correlation coeffi cient (r) equal 0.9986, coeffi cient of determination (r2) equal to 0.9973, and percentage capita

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Publication Date
Sun Nov 01 2015
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
A Comparative Study of Topical Azailic Acid Cream 20% and Active Lotion Containing Triethyl Citrate and Ethyl Linoleate in the Treatment of Mild to Moderate Acne Vulgaris
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HR Al-Hamamy, AA Noaimi, IA Al-Turfy, AI Rajab, Journal of Cosmetics, Dermatological Sciences and Applications, 2015

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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
Plasma levels and diagnostic utility of MMP-2 and TIMP-2 in the diagnosis of Iraqi women with breast tumor: A comparative study with Ca 15-3
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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
Plasma levels and diagnostic utility of MMP-2 and TIMP-2 in the diagnosis of Iraqi women with breast tumor: A comparative study with Ca 15-3
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Publication Date
Mon Jan 01 2024
Journal Name
Lecture Notes In Electrical Engineering
A Study of the Influence of Steel Brushes in Rail Surface Magnetic Flux Leakage Detection Using Finite Elements Simulation
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Publication Date
Sat Jan 02 2021
Journal Name
Journal Of The College Of Languages (jcl)
The comparative method in Maupassant’s (A woman’s Life): Le système comparatif dans Une vie de Maupassant
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The comparative method plays a major role in Maupassant’s novel (A woman’s Life).This is due to a good theme choice and smooth writing style characterized by simplicity, spontaneity and brevity.

The author uses the comparative method in the introduction of his novel where he compares the monastery’s closed world to the open world of the countryside of La Normandie, which represents the dream life of the heroine Jeanne.

The present paper is an attempt to answer the question regarding the importance of applying the comparative method in the novel (A Woman’s Life) by Maupassant. The paper stresses the fact that the novelist employs the comparative method in his book for certain features .One of these features is the

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