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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 Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
The role of the cognitive peak and its implications for achieving outstanding performanceAnalytical study of the views of a sample of the staff of the University of Baghdad
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        Knowledge represents the foundation stone for the work of all organizations, are working who leads the thinking of individuals is the ability that leads to behavior based on rationality, it is the work that creates value to the organization and thus gain access to performance winning where that knowledge is a new type of capital based on the thought and experience and is the so-called intellectual capital, which is renewable and is constantly evolving. The study sought to explain the role of the climax  knowledge in achieving the highest levels of performance Organizational and then access to the performance winning in educational organizations the study sample, was found to be a co

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Publication Date
Sat Dec 30 2023
Journal Name
Iraqi Journal Of Science
Using GPR Technique Assessment for Study the Sub-Grade of Asphalt and Concrete Conditions
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The Ground Penetrating Radar (GPR) is frequently used in pavement engineering
for road pavement inspection. The main objective of this work is to validate
nondestructive, quick and powerful measurements using GPR for assessment of subgrade
and asphalt /concrete conditions. In the present study, two different antennas
(250, 500 MHz) were used. The case studies are presented was carried in University
of Baghdad over about 100m of paved road. After data acquisition and radar grams
collection, they have been processed using RadExplorer V1.4 software
implementing different filters with the most effective ones (time zero adjustment and
DC removal) in addition to other interpretation tool parameters.
The interpretatio

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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of Some Methods for Estimating the Scheff'e Model of the Mixture
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Because of the experience of the mixture problem of high correlation and the existence of linear MultiCollinearity between the explanatory variables, because of the constraint of the unit and the interactions between them in the model, which increases the existence of links between the explanatory variables and this is illustrated by the variance inflation vector (VIF), L-Pseudo component to reduce the bond between the components of the mixture.

    To estimate the parameters of the mixture model, we used in our research the use of methods that increase bias and reduce variance, such as the Ridge Regression Method and the Least Absolute Shrinkage and Selection Operator (LASSO) method a

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Publication Date
Sun Oct 01 2023
Journal Name
Journal Of Medicine And Life
Evaluating the effect of ursodeoxycholic acid (UDCA) in comparison with dexamethasone and diclofenac in a rat model of rheumatoid arthritis
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Publication Date
Fri Aug 08 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A Comparative Evaluation of the Centering Ability and Canal Transportation of Simulated S-Shaped Canals Instrumented with Different Nickel –Titanium Rotary Systems
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Background: The purpose of this study was to evaluate and compare centering ability and canal transportation of simulated S-shaped canals instrumented with four different types of rotary nickel-titanium systems. Materials and Methods: Forty simulated S-shaped canals in resin blocks were divided into four groups of ten each and were instrumented to an apical size 25 by different instrumentation technique using ProTaper Universal files (group A), ProTaperNext (group B), Reciproc (group C) and WaveOne (group D).Centering ability and canal transportation was measured at (11) measuring points from D0 to D10 bysuperimposion of the pre- and post-operative images obtained by using digital camera in standardized manner. An assessment of the canals

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Publication Date
Thu Mar 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Administrative competencies in many of Iraqi public Organizations: comparative study.
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Competencies topic in general , and Administrative competencies in specific, are considered as important subject in the contemporary administrative literature in all countries as well as in public and privet Organizations. For this reason, we have need to study those competencies in many Iraqi Organizations.

Two Organizations wer chosen for this research one of them is the Institution of taxation, and the other is the General company of Electric the data and information related to the research have been collected by desined questioner which has been given to a sample of (50) persions divided eqully between the two maintioned organizations.

The results of the study had differences

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Publication Date
Sun Apr 01 2018
Journal Name
Journal Of Educational And Psychological Researches
Educational Thought of Ibn Sahnun and al-Kabasi: comparative study
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This study aims to illustrate and compare the perspectives of Ibn Sahnun and    al-Kabasi about educational system. To this end, the researcher adopted the inductive-analytical approach to analyze their educational perspectives. The study included two chapters: one to give an overview of the life of Ibn Sahnun and al-Kabasi and the other to analyze their perspectives. The findings revealed Ibn Sahnun and al-Kabasi confirmed that compliance with the Islamic rules is an essential condition over all aspects. As for Ibn Sahnun pointed out to the important of teaching Quran as a basic reference and guide of Muslim daily-life skills and behaviors. On the other hand, al-Kabasi focused on the creation and religion as two-main aspe

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Publication Date
Mon Jan 01 2018
Journal Name
Biochem. Cell. Arch.
Comparative anatomical study of genus Oxalis L. (Oxalidaceae) in Iraq
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The present study included the collection of fresh samples of species of genus Oxalis and examined the anatomical characteristics of the stem, scape, petiole, leaf and pedicel

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Publication Date
Sat Dec 15 2018
Journal Name
Journal Of The College Of Education For Women
Social responsibility of kindergarten teachers Eligibility and Government (Comparative Study)
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      The present research aims to identify the social responsibility of the kindergarten teachers of the civil and governmental schools (comparative study)? For the purpose of achieving the objectives of the research, the following formulas were formulated:

- Are there statistically significant differences at the level of (0.05) among the kindergarten teachers in the social responsibility scale?

 The current research was limited to kindergarten teachers (governmental and non-governmental) in the Directorate General of Education Baghdad Rusafa / Second.

The main research sample consisted of (100) teachers, (50) teachers from government kindergartens and (50) female kindergarten teache

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Publication Date
Wed Oct 11 2023
Journal Name
Journal Of Educational And Psychological Researches
Earthly Identity of Public and Private Kindergarten Children Comparative Study
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The study is concerned with the problem of the earthly identity of kindergarten children by verifying its aims in identifying the earthly identity of the first level of kindergarten children and the earthly identity of both levels of the kindergarten. The research also aims to identify the earthly identity of male and female kindergarten children. The study population is represented in public and private kindergartens on both sides of Baghdad city, Karkh & Rusafa for the academic year (2022-2023). The earthly identity test in its final form consisted of (10) items. The test was administered to a sample of (400) children in public and private kindergartens, who were selected randomly. The results showed that kindergarten children have

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