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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
Mon Sep 03 2018
Journal Name
Al-academy
The Interchange of Sign Transformation between Locality and Universality in the Iraqi Theatre, "Romeo and Juliet in Baghdad Show" - A Model
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The research deals with the interchange of the sign transformed from the universal to the local in the theatrical show through the direction processing in the production of a communicative artistic discourse and message, thus making the process of reading the speech and recognizing it by taking into account the cultural differences, customs and local rituals of each country, region, or area. The problem of the research was focused on answering the following question: What are the requirements for the sign in terms of its transformation between the universality and locality in the read-out?

               The importance of research is to determine the requiremen

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Publication Date
Mon Jan 28 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Managerial Skills and It`s Role in Strengthening the Competitive Edge of Companies: A Case Study in the General Company for Construction Industries
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This research tries to reveal how to manage and control the competitive edge for business by building managerial skills in various organizational levels. Our research aims at finding out the nature of various technical, human and in tellectual skills of a new president whose superiority is his competitive ness in the application field at general company for construe tioual  industriesand testing the surveyed minor and major changes through a questionnaire to collect information from officials. The sample was composed of (45) director. The data was analyzed  using some methods and statistical programs. The most prominent of these is (SPSS) that was used to extract the arithmetic mean, standard deviation, correlation coefficient

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Zankoy Sulaimani - Part A
A Comparison Study on the Formation of Administrative and Leadership Policies for the Team and Individual Olympic Games in the Iraqi National Olympic Committee
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The planning for the formation of administrative policies and guidance through leadership are important things for managing administrative processes and sporting activities. As both contribute in the stability of the administrative conditions, and their development in the sport federations, whether they both were attentive about team and individual Olympic Games. The two researchers observe that, there is a variation in the correct way of application. Particularly in the formulation of administrative policies and leadership describing it as, modern management standards for both team and individual Olympic Games in the Iraqi National Olympic Committee. That led to cause a misconception and lack of clarity for some administrators of those uni

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Publication Date
Sun Sep 27 2020
Journal Name
Journal Of The College Of Education For Women
Feminization and Masculinization of the Word Sun in the Holy Quran: A Semantic Study
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It is no secret for those concerned with language concerns that the issue of figurative feminization is one of the issues that does not follow a grammatical rule governed by the fact that the subject of knowledge of this is due to hearing as indicated by linguistic references and lexicons.This research opts to find out the origin of the feminization of the word sun in the Arabic language and in light of what some language specialists have argued that the origin of figurative feminization was due to non-linguistic motives related to religious and metaphysical beliefs, and that it was memory preserved in light of the linguistic heritage.The research concluded that the feminization of the sun goes back to what settled in their minds, which

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Publication Date
Sun Oct 01 2023
Journal Name
Baghdad Science Journal
Detecting DNA of multispecies dinoflagellate cysts in the sediment from three estuaries of Makassar strait and fishing port using CO1 primer: Is it CO1 primer suitable for detecting DNA dinoflagellate?
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Most dinoflagellate had a resting cyst in their life cycle.  This cyst was developed in unfavorable environmental condition. The conventional method for identifying dinoflagellate cyst in natural sediment requires morphological observation, isolating, germinating and cultivating the cysts.  PCR is a highly sensitive method for detecting dinoflagellate cyst in the sediment.  The aim of this study is to examine whether CO1 primer could detect DNA of multispecies dinoflagellate cysts in the sediment from our sampling sites. Dinoflagellate cyst DNA was extracted from 16 sediment samples. PCR method using COI primer was running. The sequencing of dinoflagellate cyst DNA was using BLAST. Results showed that there were two clades of dinoflag

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Publication Date
Mon Jan 01 2024
Journal Name
Results In Nonlinear Analysis
Numerical solutions for the time fractional Black-Scholes model governing European option by using double integral transform decomposition method
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Publication Date
Thu Jan 31 2019
Journal Name
Journal Of The College Of Education For Women
A study of some morphological characteristics of the Tigris River in the city of Baghdad
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Change the morphological characteristics with the change of the factors affecting it has been shown that the Tigris River has the characteristics of the morphology of the low values in terms of depth, width and perimeter wet and gradient which in turn affected the morphological and other characteristics in terms of the direction and pattern of runoff came through the study of 48 cross-section is taken of the Tigris River Year 2008 by section for each 1 km, it has been shown that the average width of the Tigris River does not exceed 221.1 meters and the average depth of 3.9 meters either wet ocean amounted to 268.9 meters and changed the cross-section area of the last section at a rate of 4594.3 square meters, and through the study turned

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Publication Date
Fri Jan 11 2019
Journal Name
Iraqi Journal Of Physics
A study of the effect of nano materials on the physical properties of epoxy composites
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This research studies the effect of addition of some nanoparticles
(MgO, CuO) and grain size (30,40nm) on some physical properties
(impact strength, hardness and thermal conductivity) for a matrix
blend of epoxy resin with SBR rubber. Hand –Lay up method was
used to prepare the samples. All samples were immersed in water for
9 weeks.
The Results showed decreased in the values of impact strength and
hardness but increased the coefficient of thermal conductivity.

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Publication Date
Sat Sep 30 2023
Journal Name
Al–bahith Al–a'alami
The Role of Website Users in the Consumption of Notifications: A Field Study of Websites
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This research seeks to explore the impact of notifications on enhancing user engagement with websites, primarily through user subscriptions and their interaction with notifications on these websites. The significance of this study lies in its implications for crafting compelling headlines that capture users' attention, streamline their access to journalistic content, and align with the objectives and editorial policies of news websites. It sheds light on the factors influencing users' preferences for specific notifications and their engagement with content based on their individual interests, motivations, and the satisfaction derived from such interactions.
The researcher has reached several key findings, inc

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Publication Date
Wed Jan 30 2013
Journal Name
Al-kindy College Medical Journal
Paraphilia in Iraq, a general sketch A study in the sex clinic, at Al-Rashad teaching mental hospital
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Background; paraphilias were studied in the sex
clinic, at Al-Rashad teaching mental hospital, in the
years 2009-2010, a subject never touched before in the
field of psychiatry in Iraq.
Aims of the study :
1-to identify the prevalence of types and number of
paraphilias in those patients.
2-to study the relationship of paraphilias with
sociodemographic factors of the patients.
Patients and methods; using the diagnostic criteria of
DSM IV TR, 52 patients from the outpatient sex clinic
at Al-Rashad mental hospital, collected and studied (41
males and 11 females).
Results; the ratio of men to women was 3.7 : 1, the
majority of our sample was in the age range of 21-30
years (36.35%), with a limited

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