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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
Sat Aug 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
A conceptual Framework For the Relationship between Human and Social Capital
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Purpose: The research seeks to develop the implications of intellectual human capital, and social capital in business organizations, and will be accomplished on three levels, the first level (the level of description) to identify, diagnose and display content philosophical Strategic Human Resource Management at the thought of modern administrative represented by human capital and Ras social capital. The second level (level of analysis) and the analysis of the extent of the impact of alignment between human capital, and social capital in the organizational strength of the organizations. The third level (Level predict) the formulation of a plan to strengthen the organizational strength in business organizations and to develop speci

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Publication Date
Sat Sep 04 2021
Journal Name
Neuroquantology
Nanotechnology and the Most Important Characterization Techniques for Nanomaterial's: A Review
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Due to the importance of nanotechnology because of its features and applications in various fields, it has become the focus of attention of the world and researchers. In this study, the concept of nanotechnology and nanomaterials was identified, the most important methods of preparing them, as well as the preparation techniques and the most important devices used in their characterization.

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Publication Date
Tue Mar 01 2022
Journal Name
International Journal Of Nonlinear Analysis And Applications
The suggested threshold to reduce data noise for a factorial experiment
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In this research, a factorial experiment (4*4) was studied, applied in a completely random block design, with a size of observations, where the design of experiments is used to study the effect of transactions on experimental units and thus obtain data representing experiment observations that The difference in the application of these transactions under different environmental and experimental conditions It causes noise that affects the observation value and thus an increase in the mean square error of the experiment, and to reduce this noise, multiple wavelet reduction was used as a filter for the observations by suggesting an improved threshold that takes into account the different transformation levels based on the logarithm of the b

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Publication Date
Thu Feb 15 2024
Journal Name
Journal Of Theoretical And Applied Information Technology
CHOOSING THE RIGHT CHAOTIC MAP FOR IMAGE ENCRYPTION: A DETAILED EXAMINATION
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This article investigates how an appropriate chaotic map (Logistic, Tent, Henon, Sine...) should be selected taking into consideration its advantages and disadvantages in regard to a picture encipherment. Does the selection of an appropriate map depend on the image properties? The proposed system shows relevant properties of the image influence in the evaluation process of the selected chaotic map. The first chapter discusses the main principles of chaos theory, its applicability to image encryption including various sorts of chaotic maps and their math. Also this research explores the factors that determine security and efficiency of such a map. Hence the approach presents practical standpoint to the extent that certain chaos maps will bec

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Publication Date
Fri Feb 08 2019
Journal Name
Journal Of The College Of Education For Women
The American Occupation Policy toward Japan 1945-1951 and Iraq 2003-2008: Comparative Historical Study
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With their strategic and geographical positions, Japan and Iraq are one of the major
countries in the world, especially to the United States. Japan lies near the two American
Continents, separated only by the Pacific and it is only normal to have the interests of both
countries crossed and joined in the Far East region. This made the occupation of Japan an
inventible matter in the second half of the 20th century. Iraq, on the other hand, has strategic
position in the Middle East, being surrounded by many active countries like Turkey, Iran, and
Gulf countries, besides Iraq’s oil wealth which is needed by such industrial country like the
United States.

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Publication Date
Sat Nov 22 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An in-vitro scan electron microscope comparative study of dentine-Biodentine interface
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Background: Restoration of the gingival margin of Class II cavities with composite resin continues to be problematic, especially where no enamel exists for bonding to the gingival margin. The aim of study is to evaluate the marginal leakage at enamel and cementum margin of class II MOD cavities using amalgam restoration and modern composite restorations Filtek™ P90, Filtek™ Z250 XT (Nano Hybrid Universal Restorative) and SDR bulk fill with different restoratives techniques. Materials and method: Eighty sound maxillary first premolar teeth were collected and divided into two main groups, enamel group and cementum group (40 teeth) for each group. The enamel group was prepared with standardized Class II MOD cavity with gingival margin (1 m

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Publication Date
Wed Aug 02 2023
Journal Name
Bionatura
Comparative Study of IgG Between Iraqi Covid-19 Patients and Vaccinated Individuals
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COVID-19 is a coronavirus disease caused by the severe acute respiratory syndrome. According to the World Health Organization (WHO), coronavirus-2 (SARS-CoV-2) was responsible for 87,747,940 recorded infections and 1,891,352 confirmed deaths as of January 9, 2021. Antibodies that target the Sprotein are efficient in neutralizing the virus. Methodology: 180 samples were collected from clinical sources (Blood and Nasopharyngeal swabs) and from different ages and genders at diverse hospitals in Baghdad / IRAQ between November 5, 2021, to January 20, 2022. All samples were confirmed infected with COVID-19 disease by RT-PCR technique. Haematology analysis and blood group were done for all samples, and Enzyme-Linked Immunosorbent Assay used an Ig

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Publication Date
Wed Dec 30 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study of New Re-Ni-Mo/Al2o3 and Conventional Hydrodesulphurization Catalyst
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New types of hydrodesulfurization (HDS) catalyst Re-Ni-Mo/ γ-Al2O3 was prepared and tested separately with two prepared conventional HDS catalysts (Ni-Mo/ γ-Al2O3 and Co-Mo//γ-Al2O3) by using a pilot plant hydrotreatment unit. Activities of three prepared hydrodesulfurization catalysts were examined in hydrodesulfurization (HDS) of atmospheric gas oil at different temperatures 275 to 350 °C and LHSV 1 to 4 h-1, the reactions conducted under constant pressure 40 bar and H2/HC ratio 500 ml/ml .Moreover, the hydrogenation of aromatic (HAD) in gas oil has been studied. HDS was much improved by adding promoter Re to the Ni-Mo/Al2O3 catalyst. The results showed that Re-Ni-Mo/ γ-Al2O3 have more activity in desulfurization than Ni-Mo//γ-Al2O3

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Publication Date
Mon Jun 03 2019
Journal Name
Rawal Medical Journal
SUPERIOR VERSUS ANTERIOR PLATING OF MIDSHAFT CLAVICLE FRACTURE IN ADULT COMPARATIVE STUDY
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Clavicle fractures are common injuries in young, active individuals. The majority of the fractures (80% to 85%) occur in the mid-shaft of the bone and account for approximately 2.6% of all fractures. For many years the standard treatment of fracture clavicle was the "figure-of-eight" bandage but several indications for operative fixation, the position of plate fixation for clavicle fracture remains controversial. The aim of this study is to compare between anterio—inferior and anterior-superior plating of mid-shaft displaced clavicle fracture in complications, plate prominence, nonunion, malunion and range of motion. This study is a prospective study conducted in Al-Kindy teaching hospital .A total of 30 patients with fracture mid –sh

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Publication Date
Thu Dec 31 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study of New Re-Ni-Mo/Al2o3 and Conventional Hydrodesulphurization Catalyst
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New types of hydrodesulfurization (HDS) catalyst Re-Ni-Mo/ γ-Al2O3 was prepared and tested separately with two prepared conventional HDS catalysts (Ni-Mo/ γ-Al2O3 and Co-Mo//γ-Al2O3) by using a pilot plant hydrotreatment unit. Activities of three prepared hydrodesulfurization catalysts were examined in hydrodesulfurization (HDS) of atmospheric gas oil at different temperatures 275 to 350 °C and LHSV 1 to 4 h-1, the reactions conducted under constant pressure 40 bar and H2/HC ratio 500 ml/ml .Moreover, the hydrogenation of aromatic (HAD) in gas oil has been studied. HDS was much improved by adding promoter Re to the Ni-Mo/Al2O3

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