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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 Dec 31 2018
Journal Name
Ibn Al-haitham Jour. For Pure & Appl. Sci
Comparative Study of Thymidine Kinase -1 and Total Antioxidant Capacity in Iraqi Children with Platelet Count Disorder
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This study aimed to find relationship between thymidine kinase-1 (TK-1) as tumor marker and total antioxidant capacity (TAC) in Iraqi children patients with thrombocytopenia and with thrombocytosis. The present study conducted 60 children patients (30 patients with idiopathic thrombocytopenia purpura (ITP) and 30 patients with thrombocytosis caused by leukemia) attending the Children Fever Hospital in the Medical City / Baghdad, and 30 healthy children as a control group. All study groups were with range ages (1-15) years, and they were diagnosed by assay of platelet count, Prothrombin Time (PT), and partial Thromboplastin Time (PTT). The results shown elevation in plasma TK-1 and TAC values in children patients with thrombocytopenia and w

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Publication Date
Thu May 30 2024
Journal Name
Proximus Journal Of Sports Science And Physical Education
A COMPARATIVE STUDY OF THE MOST IMPORTANT PERSONALITY TRAITS BETWEEN PRACTITIONERS AND NON-PRACTITIONERS OF SPORTS ACTIVITY
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The researchers reached many conclusions, the most important of which was the distinction of practitioners of sports activity with high degrees in the trait (social). At the same time, it was low in the trait (aggression –restraint-desisting) and non-practitioners were distinguished by sports activity with high degrees in the trait (aggression –restraint-desisting). In contrast, the degree was low in the trait (social), and there were significant differences in favor of practitioners of the activity of the athlete, Through the conclusions, the researchers recommend the need for university students to practice sports activities because of their positive impact on their health in general and on the deve

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Publication Date
Tue Apr 01 2025
Journal Name
Iop Conference Series: Earth And Environmental Science
A Comparative Study of Organic and Mineral Acids in the Release of Potassium from Potassium Feldspar Minerals
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Abstract<p>A study conducted a laboratory experiment to measure the release of potassium and the dissolution of feldspar minerals in soils from different locations in Karbala Province (Ain Al-tamur, Qasr Al-Akhyar, Fadak Farm). The study involved the addition of organic acids (fulvic and humic) and mineral acids (sulfuric and phosphoric) at concentrations of 5% and 10% to sand-separated soil samples obtained through wet sieving. Feldspar minerals were identified using a polarized light microscope, and the percentage of each type of feldspar mineral was calculated. The results demonstrated that organic acids outperformed mineral acids in releasing potassium at both concentrations. Among the organ</p> ... Show More
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Publication Date
Thu Nov 01 2012
Journal Name
Journal Of The Faculty Of Medicine Baghdad
A Comparative Study of the Effects of Age and Smoking on Nail Growth Rate in Healthy Individuals
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GA Al Omran, AA Noaimi, Z Al Madfai, H Al Hamamy, Journal of the Faculty of Medicine Baghdad, 2012

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
A comparative study of the effects of argon laser and continuous Nd: YAG laser on blood vessel
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Several types of laser are used in experimental works in order to study the effects of laser on blood vessel. They differ from each other by a lot of properties mainly in wavelength, energy of the laser and pulse duration. In this study argon laser (488 nm- 514 nm) and continuous Nd: YAG laSer (1064 nm), have been applied to 50 samples of sheep blgod tesselS. Histologically, tha results of the study were different According to the txpe of L`sar used; apgon larer had distrabtave effects on $he blood vessal while continuous Nd: YAG laser Appeaped to be the safesd one on the blmod vessel architecture. This study concluded that argoj laser has da-aging ef&ect on

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Publication Date
Wed Jul 01 2020
Journal Name
Plant Archive
A comparative taxonomic study of seeds of some plants of rosaceae family in Iraq
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Publication Date
Mon Nov 17 2025
Journal Name
Al–bahith Al–a'alami
Selective Exposure Patterns to the Iraqi Daily Newspapers and Its Motives for Iraqi University Students (College of Mass Communication - University of Baghdad as a Model)
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This study examines patterns of exposure of Iraqi university students to selective daily Iraqi newspapers and the motives of this exposure, as well as its associated factors that affect the average exposure. It tries to answer several questions, including those related to the levels of exposure of Iraqi university students to daily Iraqi newspapers and classification of patterns of selective exposure to daily Iraqi newspapers and the most prominent Iraqi daily newspapers that are selectively exposed by Iraqi university students. It also examines the motives of this selective exposure and factors that increase the degree of exposure to the daily Iraqi newspapers, and the most prominent stages in which Iraqi university students find their

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Publication Date
Thu Nov 02 2023
Journal Name
Journal Of Engineering
Constructing a Sustainable Roller Compacted Concrete Using Waste Demolished Material as Replacement of Cement: A Review
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Roller Compacted Concrete is a type of concrete that is environmentally friendly and more economical than traditional concrete. Roller Compacted Concrete is typically used for heavy-duty and specialist constructions, such as hydraulic structures and pavements, because of its coarse surface. The main difference between RCC and conventional concrete mixtures is that RCC has a more significant proportion of fine aggregates that allow compaction and tight packing. In recent years, it has been estimated that several million tons of waste demolished material (WDM) produced each year are directed to landfills worldwide without being recycled for disposal. This review aimed to study the literature about creating a Roller-Comp

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Publication Date
Mon Aug 18 2025
Journal Name
Journal Of Genetic And Environment Conservation
Ultrasound application as a new green technology for preservation of table eggs: A review
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In recent years, there has been a significant increase in research demonstrating the new and diverse uses of non-thermal food processing technologies, including more efficient mixing and blending processes, faster energy and mass transfer, lower temperature and selective extraction, reduced thermal and concentration gradients, reduced equipment size, faster response to extraction control, faster start-up, increased production, and a reduction in the number of steps in preparation and processing. Applications of ultrasound technology have indicated that this technology has a promising and significant future in the food industry and preservation, and there is a wide scope for its use due to the higher purity of final products and the

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Publication Date
Thu Jan 16 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Technological Literacy in Educational Programs in The Department of Accounting: As one of the Resources of Human Development
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Education is considered the corner stone of all nations development. It is the principal way for the development of human sources and the most achievements of the age due to the knowledge of these resources .                                           

   As its active role which accounting departments implement in Iraq universities , (public and private) through their teaching programs , they aim to supply labour-market with qualified cadre graduated as accountants auditors , tax auditors , financial analysts , ac

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