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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 Sep 30 2015
Journal Name
European Journal Of Chemistry
Reaction pathways and transition states of the C-C and C-H bond cleavage in the aromatic pyrenemolecule - A Density Functional study
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The activation and reaction energies of the C-C and C-H bonds cleavage in pyrene molecule are calculated applying the Density Functional Theory and 6-311G Gaussian basis. Different values for the energies result for the different bonds, depending on the location of the bond and the structure of the corresponding transition states. The C-C bond cleavage reactions include H atom migration, in many cases, leading to the formation of CH2 groups and H-C≡C- acetylenic fragments. The activation energy values of the C-C reactions are greater than 190.00 kcal/mol for all bonds, those for the C-H bonds are greater than 160.00 kcal/mol. The reaction energy values for the C-C bonds range between 56.497 to 191.503 kcal/mol. As for the C-H cleavage rea

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Publication Date
Mon Sep 01 2025
Journal Name
Journal Of Dentistry
Influence of zirconia thickness and background color on color matching accuracy of monolithic zirconia restorations
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objective: To evaluate the influence of monolithic zirconia brand, thickness, and substrate color on color matching accuracy when optically coupled to abutment substrates. Methods: A total of 180 samples of two brands of monolithic zirconia [Prettau Anterior (PA), Ceramill Zolid FX Multicolor (CZ)] were prepared in three different thicknesses (0.8 mm, 1.5 mm, and 2 mm) with a standardized 10 mm diameter. Color properties of the samples were assessed using spectrophotometry at baseline and after coupling to three substrate types: standard dentin, discolored dentin, and titanium. Color differences (ΔE) were calculated and statistically analyzed by 3-way ANOVA and pairwise comparison ( α=0.05). Results: The brand and material thickness, at

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Publication Date
Sun Mar 03 2013
Journal Name
Baghdad Science Journal
Study the Spectral reflectance and factor affecting they for the dominate land cover by using remote sensing technique in Abu-Gharib projection.
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Image of landsate-7 taken by thematic mapper was used and classified using supervised method. Results of supervised classification indicated presence of nine land cover classes. Salt-soils class shows the highest reflectance value while water bodies' class shows the lowest values. Also the results indicated that soil properties show different effects on reflectance. There was a high significant positive relation of carbonate, gypsum, electric conductivity and silt content, while there was a week positive relation with sand and negative relation with organic matter, water content, bulk density and cataion exchange capacity.

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Publication Date
Tue Jan 01 2013
Journal Name
Journal Of The College Of Basic Education
Study the spectral reflectance and factor affecting they for the dominate land cover by using remote sensing technique in Abu-Gharib projection
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Image of landsate-7 taken by thematic mapper was used and classified using supervised method. Results of supervised classification indicated presence of nine land cover classes. Salt-soils class shows the highest reflectance value while water bodies' class shows the lowest values. Also the results indicated that soil properties show different effects on reflectance. There was a high significant positive relation of carbonate, gypsum, electric conductivity and silt content, while there was a week positive relation with sand and negative relation with organic matter, water content, bulk density and cataion exchange capacity.

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Publication Date
Tue Oct 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The Time-Cost Trade-off to Manage A Project in a Fuzzy Environment
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In this research, the problem of ambiguity of the data for the project of establishing the typical reform complex in Basrah Governorate was eliminated. The blurry of the data represented by the time and cost of the activities was eliminated by using the Ranking function and converting them into normal numbers. Scheduling and managing the Project in the Critical Pathway (CPM) method to find the project completion time in normal conditions in the presence of non-traditional relationships between the activities and the existence of the lead and lag periods. The MS Project was used to find the critical path. The results showed that the project completion time (1309.5) dinars and the total cost has reached (33113017769) dinars and the

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Publication Date
Sun Mar 01 2026
Journal Name
Journal Of Baghdad College Of Dentistry
The effect of different oral hygiene regimens on the quantity of cariogenic plaque on orthodontic bands with different attachments (A clinical photographic study)
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Background: Fixed orthodontic appliances impede the maintenance of oral hygiene and result in plaque accumulation leads to enamel demineralization caused by acids produced by bacteria. Studies on plaque control strategies in orthodontic populations are limited. This might be caused by difficulties in the quantitative evaluation of dental plaque because the teeth have various levels of bracket coverage, and different tooth sizes and malocclusions, making the traditional categorical indices complex. The present study aims to evaluate the effect of different hygiene protocols on plaque quantity on bands with different attachments. Materials and method: Twenty patients had four bands within the orthodontic appliance. Then randomly divided into

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Publication Date
Sat Jun 26 2021
Journal Name
Journal Of The College Of Education For Women
Education and the Challenges of Globalization during the Corona Pandemic: A Field Study from Baghdad University Professors’ Point of View: ميسم ياسين عبيد
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study aims to examine education and the challenges of globalization in light of Corona pandemic. The examination involves surveying a randomly selected sample from the University of Baghdad’s professors, particularly from the colleges of Education for Women, Arts, and Sciences. The purpose of this examination is to learn about the dimensions of globalization, its effects on the educational process, and the importance of distance education during the spread of Corona virus quarantine. To achieve this, the researcher followed a descriptive and analytical approach by applying a questionnaire to a sample of 70 teachers who were randomly selected electronically. Results have shown that 78.6% emphasized the contribution of globalization duri

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Publication Date
Fri Aug 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
The role of intellectual capital in promoting financial performance an applied study on a sample of the companies listed in Iraq stock exchange
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The interest in the intellectual capital and its development is a civilized necessity imposed by the requirements of the times and cannot imagine an advanced society in its potential productivity in poor efficiency of human capital, and features the work environment change permanently, putting the management of financial companies against a constant challenge toward coping with new developments in this changing environment and this is not taken unless owned by these companies qualified human resources and the provision of Culture organizers have, which manifested itself with the research problem by the following two questions:

  1. Did the intellectual capital value specific financial and

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Publication Date
Tue Jan 01 2013
Journal Name
العلوم التربوية والنفسية
The effect of a strategy for creative thinking on the achievement of chemistry and the reading comprehension ability of secondary school female students
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Publication Date
Mon Jun 30 2025
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
USE OF SHRIMP WASTE POWDER (METAPENAEUS AFFINIS) AND PROTEASE ENZYME IN BROILERS FEED AND ITS EFFECT ON PHYSIOLOGICAL AND MICROBIAL CHARACTERISTICS AND INDICATORS OF FAT OXIDATION IN MEAT
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This study was conducted in the poultry field of the Department of Animal Production/ College of Agricultural Engineering Sciences / University of Baghdad for the period from 42 days. Aiming to know the effect of using shrimp waste powder (Metapenaeus Affinis) and enzyme in broilers diet on physiological and microbial performance and indicators of fat oxidation in meat. 250 one-day-old ROSS308 chicks were used. The chicks were fed on diets containing shrimp waste treated with enzyme and not treated with protease enzyme by 0,4,6 %. The experiment included five treatments, with 5 replicates for each treatment, and each replicate contained 10 birds. The results showed a significant decrease (P≤0.05) in the concentration of ALT and AS

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