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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
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
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
Mon Jan 01 2018
Journal Name
African Journal Of Hospitality, Tourism And Leisure
An analytical study of the strategic flexibility variation as a function of the dynamic capabilities based on supply chain management (Case study: The General Petroleum Products Distribution Company in Baghdad)
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Publication Date
Fri Mar 22 2019
Journal Name
Journal Of Pharmaceutical Sciences And Research
Evaluation of the efficacy of caries removal using papain gel (Brix 3000) and smart preparation bur (in vivo comparative study)‏
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Publication Date
Wed Jun 28 2023
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
PREPARATION OF A COMBINATION OF NANO- MEDICINAL PLANTS AS ANTIOXIDANTS AND MICROORGANISMS: PREPARATION OF A COMBINATION OF NANO- MEDICINAL PLANTS AS ANTIOXIDANTS AND MICROORGANISMS
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ABSTRACT

            The controversy is currently revolving around industrial additives, including antioxidants, their negative effects on consumer health and the emergence of various and various diseases, which led scientists and researchers to intensify most studies on natural antioxidants and their synthesis from medicinal plants mentioned in ancient medicine and in divine books as potential antioxidants of increasing importance. Therefore, this study was designed to synthesize silver nitrate particles from plant leaf extracts (Figs, Olives, and Moringa) and study their effect on bacterial inhibition of each of the undesirable Coliform bacteria (E-Coli,

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Publication Date
Mon Aug 31 2020
Journal Name
Bmc Oral Health
The success of using 2% lidocaine in pain removal during extraction of mandibular premolars: a prospective clinical study
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Abstract<sec><title>Background

The purpose of this study was to evaluate the anesthetic effectiveness of a buccal infiltration technique combined with local massage (using 2% lidocaine) in the extraction of mandibular premolars to be utilized as an alternative to the conventional inferior alveolar nerve block.

Methods

Patients eligible included any subject with a clinical indication for tooth extraction of the mandibular 1st or 2nd premolars. All patients were anesthetized buccally by local infiltration technique followed by an external pressure applied for 1 min directly over the injection area. In each case, another local

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Publication Date
Thu Jan 22 2026
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
Sun Dec 13 2020
Journal Name
Clinical And Experimental Dental Research
The efficacy of polyether‐ether‐ketone wire as a retainer following orthodontic treatment
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Abstract<sec><title>Objectives

To investigate the efficacy of polyether‐ether‐ketone (PEEK) wire as a fixed orthodontic retainer, by comparing its performance to other retainer wires and optimizing its adhesion to composite bonding materials.

Materials and methods

Retainer wires of 15 mm segments were used, PEEK wires were prepared in cylindrical form with 0.8 mm diameter, and had two surface treatments namely air‐abrasion and conditioning with adhesive system. Three different metallic retainer wires were used for comparison and three tests were performed; two tests measured debonding force and associated wire deflec

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