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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
Thu Dec 01 2016
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
THE OCCURRENCE OF THREE MONOGENEAN PARASITE SPECIES FOR THE FIRST TIME IN IRAQ ON GILLS OF THE COMMON CARP CYPRINUS CARPIO LINNAEUS, 1758 (CYPRINIFORMES, CYPRINIDAE)
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    The monogeneans Gyrodactylus dzhalilovi Ergens & Ashurova, 1984, G. magnus Konovalov, 1967 and G. matovi Ergens & Kakachava-Avramova, 1966 were recorded in this study for the first time in Iraq from gills of the common carp Cyprinus carpio Linnaeus, 1758 collected from Tigris River in Baghdad city. The description, measurements and illustrations of these parasites were given.

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Publication Date
Thu Apr 08 1999
Journal Name
Abhath Al- Yarmouk [basic Sciences And Engineering]
Model for Predicting the Cracking Moment in Structural Concrete Members
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Publication Date
Tue May 16 2023
Journal Name
Journal Of Engineering
Statistical Model for Predicting the Optimum Gypsum Content in Concrete
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The problem of internal sulfate attack in concrete is widespread in Iraq and neighboring countries.This is because of the high sulfate content usually present in sand and gravel used in it. In the present study the total effective sulfate in concrete was used to calculate the optimum SO3 content. Regression models were developed based on linear regression analysis to predict the optimum SO3 content usually referred as (O.G.C) in concrete. The data is separated to 155 for the development of the models and 37 for checking the models. Eight models were built for 28-days age. Then a late age (greater than 28-days) model was developed based on the predicted optimum SO3 content of 28-days and late age. Eight developed models were built for all

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Publication Date
Thu Oct 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Choose the best model for building life tables in Iraq
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Demography or population studies or demography is the science that is based on the different characteristics of the population scientific study, and represent a population studies principled way to understand the population of society, in addition to verification of the population in a given area determine the reason for the increase or decrease this number from the previous statistical As these studies estimate future trends for the occurrence of demographic change in terms of birth, death and migration That the registration of deaths of paramount importance narrated that way can the demographic reality of the population analysis, and coverage of the health authorities' needs and enable government institutions of decision-making

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Publication Date
Tue Dec 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
The role of MIS in the negotiation process "An Analytical Study in a Sample of Iraqi Organizations"
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Negotiation is considered as one of the most important kinds of communication in the contemporary organizations, which depend on the important role of managerial information systems in providing necessary and suitable information for success of the negotiation process.

Accordingly, this study aims at measuring the extent of the variables effect of managerial information system in the negotiation process.

To achieve this study, two hypotheses were chosen; the first is the correlation relation and the second is the effect, and statistical means represented by correlation coefficient "Spearman" and (R2) were used.

 A Number of conclusions were

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Publication Date
Wed Feb 22 2023
Journal Name
Iraqi Journal Of Agricultural Sciences
A STUDY OF ECONOMIC, SOCIAL, AND INSTITUTIONAL FACTORS AFFECTING THE ADOPTION OF THE HIGH-RANK WHEAT SEEDS
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The aim of this research is to investigate the effect of economic, social and institutional factors on adoption within the national program for the propagation of high-rank seeds of wheat crop. 170 questionnaires were collected, 50% of them were participants in the program from Wasit and Babil governorates. Probabilistic regression models were used to know this effect, and the possibility of adopting Farmers of improved seeds produced from the national program for the multiplication of seeds of higher grades using the (ADOPT) program. The adoption rate was 0.12%, and the total number of adopters were 12 farmers, at a rate of 14.2%. Tobit model was estimated  to find out the impact of the profitability of the dunum, capital, farm si

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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of Research In Medical And Dental Science
The Efficacy of 4% Articaine Infiltration Anesthesia in the Extraction of Mandibular Molars: A Randomized Controlled Study
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Introduction: Articaine was developed in 1969, with reported advantages which are increased potency, increased duration of its anesthetic effect and superior diffusion through bony tissue. The effectiveness of using 4% articaine infiltration for extraction of mandibular molar teeth in comparison to 2% lidocaine inferior alveolar nerve block is not settled yet. Aim: The aim of this study was to evaluate the effectiveness of using 4% articaine infiltration for extraction of mandibular molars by comparing it to the use of 2% lidocaine inferior alveolar nerve block in terms of success, the volume of local anesthetic agents and the pain experienced during the procedure. Materials and methods: A prospective randomized controlled study included

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Publication Date
Wed Dec 15 2021
Journal Name
Al-academy
The role of psychological content in building the fiction film an analytical study of a selected sample
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 Psychological aspects are a major influence and motivation factor in many cinematic and television works such as television series. There are many films that dealt with psychological issues through the personality affected by psychological projections and complexes that lead towards abnormal behavior and actions in most cases, so the researchers chose the title and the research problem was raised through the following question: What is the mechanism that fulfills a psychological role in the narrative film? The objectives of the research were to reveal the mechanism used to instill psychological contents in the feature film? As for the limits of the research, it was an intentional sample, and the researchers adopted the descriptive anal

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Publication Date
Wed May 08 2024
Journal Name
Journal Of Mathematics And Computer Science
How does media coverage affect a COVID-19 pandemic model with direct and indirect transmission?
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In this paper, a compartmental differential epidemic model of COVID-19 pandemic transmission is constructed and analyzed that accounts for the effects of media coverage. The model can be categorized into eight distinct divisions: susceptible individuals, exposed individuals, quarantine class, infected individuals, isolated class, infectious material in the environment, media coverage, and recovered individuals. The qualitative analysis of the model indicates that the disease-free equilibrium point is asymptotically stable when the basic reproduction number R0 is less than one. Conversely, the endemic equilibrium is globally asymptotically stable when R0 is bigger than one. In addition, a sensitivity analysis is conducted to determine which

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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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