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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
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Detection capability Alttafaria for some materials using a bacterial mutagenesis system
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Tested effective Alttafaria some materials used for different purposes, system a bacterial mutagenesis component of three bacterial isolates belonging to different races and materials tested included drug Briaktin

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Publication Date
Tue Dec 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of ageing media on shear bond strength of metal orthodontic brackets bonded with different adhesive systems (A comparative in-vitro study)
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Background: The aim of this study was to evaluate the shear bond strength (SBS) and adhesive remnant index (ARI) of different orthodontic adhesive systems after exposure to aging media (water storage and acid challenge). Materials and methods: Eighty human upper premolar teeth were extracted for orthodontic purposes and randomly divided into two groups (40 teeth each): the first group in which the bonded teeth were stored in distilled water for 30 days at 37°C, and the second group in which the bonded teeth were subjected to acid challenge. Each group was further subdivided into four subgroups (10 teeth each) according to the type of adhesive system that would be bonded to metal brackets: either non-fluoride releasing adhesive (NFRA),

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Publication Date
Tue Dec 26 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
A Comparative Study of Blood Levels of Manganese, Some Macroelements and Heavy Metals in Obese and Non-Obese Polycystic Ovary Syndrome Patients
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Polycystic ovary syndrome (PCOS) is a prevalent condition in women of reproductive age. It is characterized by androgen excess and chronic anovulation. Some trace elements, macroelements, and heavy metals have been linked to pathophysiological mechanisms of PCOS .

To study the alterations in the serum levels of the trace element manganese (Mn), some macroelements, magnesium(Mg) and calcium (Ca), and the heavy metals cadmium (Cd) and lead (Pb), in obese and non-obese PCOS patients; and the association of these alterations with some of the hormonal changes occurring in PCOS.

The study was carried out at Kamal Al-Samarrai Hospital (Center for Infertility treatment and in vitro Fertilization "IVF") Baghdad- Iraq. Eig

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Publication Date
Fri Oct 04 2024
Journal Name
Chemical Review And Letters
Newly designed 2-(aminomethyl)benzimidazole derivatives as possible tyrosine kinase inhibitors: synthesis, characterization, preliminary cytotoxic evaluation and in Silico studies
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Publication Date
Fri May 01 2020
Journal Name
Journal Of Engineering
A Study of the Hydrodynamics Behavior of Cylindrical Gas-Solid Fluidized Beds for pharmaceutical material “Paracetamol “
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The hydrodynamics behavior of gas - solid fluidized beds is complex and it should be analyzed  and understood due to its importance in the design and operating of the units. The effect of column inside diameter and static bed height on the minimum fluidization velocity, minimum bubbling velocity, fluidization index, minimum slugging velocity and slug index have been studied experimentally and theoretically for three cylindrical columns of 0.0762, 0.15 and 0.18 m inside diameters  and 0.05, 0.07 and 0.09 m static bed heights .The experimental results showed that the minimum fluidization and bubbling velocities had a direct relation with column diameter and static bed height .The minimum slugging velocity had an

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Publication Date
Mon Apr 20 2020
Journal Name
International Medical Journal
Cleaning efficacy and instrumentation time using rotary file system in primary molars (comparative study)
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ABSTRACT— In primary teeth, root canal treatment is a time consuming and challenging procedure, particularly during the most important step in endodontic treatment which is the preparation of the canal. Pulpectomy is the treatment of choice in all the necrotic primary teeth. For better treatment protocol, advancing technology brought the rotary system to reduce the manual dexterity and improve the quality of treatment for pulpectomy. This study aimed to compare and assess the efficacy of cleaning and the time required for the instrumentation during the preparation of root canals of the primary molars using the rotary and the manual (conventional) systems. Thirty root canals of primary teeth were selected. These teeth submitted to a

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Publication Date
Tue Jul 01 2014
Journal Name
International Journal Of Artificial Intelligence And Mechatronics
Machining Polylines and Ellipses using Three-Axis CNC Milling Machine
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CNC machine is used to machine complex or simple shapes at higher speed with maximum accuracy and minimum error. In this paper a previously designed CNC control system is used to machine ellipses and polylines. The sample needs to be machined is drawn by using one of the drawing software like AUTOCAD® or 3D MAX and is saved in a well-known file format (DXF) then that file is fed to the CNC machine controller by the CNC operator then that part will be machined by the CNC machine. The CNC controller using developed algorithms that reads the DXF file feeds to the machine, extracts the shapes from the file and generates commands to move the CNC machine axes so that these shapes can be machined.

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Publication Date
Fri Aug 22 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Nasopharyngeal Dimensions in Relation to Some Dento-Cranial Variables in Class I and II Skeletal Patterns (A Comparative Cephalometric Study)
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Background: The size of the nasopharyngeal airway was believed to have an important role in the development of the dentofacial structure. This study was carried out to test the relation between the nasopharyngeal dimensions with some dento-cranial measurements in class I and II jaw relationship. Materials and Methods: This study was done on 60 subjects (30 males and 30 females) at age range 18-25 years. Cephalometric radiograph has been taken to each subject and the measurements were recorded. The sample was divided into two groups, class I skeletal relationship (15 males and 15 females) and class II skeletal relationship (15 males and 15 females). Comparisons between the different study groups were undertaken. Results: In class I skeletal

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Publication Date
Sun Jun 07 2015
Journal Name
Baghdad Science Journal
A comparative study between conventional methods and Vidas UP Salmonella (SPT) to investigate salmonella species from local and imported meat
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The study was preformed for investigating of Salmonella from meat, and compared Vidas UP Salmonella (SPT) with the traditional methods of isolation for Salmonella , were examined 42 meat samples (Beef and Chicken) from the Local and Imported From local markets in the city of Baghdad from period December 2013 -February 2014 the samples were cultured on enrichment and differential media and examined samples Vidas, and confirmed of isolates by cultivation chromgenic agar, biochemical tests ,Api20 E systeme , In addition serological tests , and the serotypes determinate in the Central Public Health Laboratory / National Institute of Salmonella The results showed the contamination in imported meat was more than in the local meat 11.9% and 2

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Publication Date
Thu Oct 01 2009
Journal Name
Iraqi Journal Of Physics
PMMA/ Anthracene Film as a Low Doses Dosimeter
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A prepared PMMA/Anthracene film of thickness 70μm was irradiated under reduced pressure ~10-3 to 60Coγ-ray dose of (0.1mrad-10krad) range. The optical properties of the irradiated films were evaluated spectrophotometrically. The absorption spectrum showed induced absorption changes in the 200-400nm range. At 359nm, where there is a decrease in radiation-induced absorption, the optical density as a function of absorbed dose is linear from 10mrad-10Krad.It can therefore, be used as radiation dosimeter for gamma ray in the range 10mrd-10krad

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