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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
Thu Dec 13 2018
Journal Name
Al-adab Journal
A Victim of "Love": A Study of Beatrice’s Character in "Rappaccini's Daughter" By Nathanial Hawthorne
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Nathaniel Hawthorne (1804-1864) has been widely known for his special interest in the female characters. In many of his novels, he narrates the conditions, values, and the institutions that surround and control the life of women, leading them to be victims. In “Rappaccini’s Daughter” (1844), the heroine, Beatrice is created to be victimized by her loved ones (her father and lover). This paper focuses on the term “victim,” it shows its aspects through the development of Beatrice’s character. The paper also studies a female character in the male-dominated society, to show the cruelty done to her, and how she is considered to be a second rate person, who is unable to live normally, or at least to save herself from dea

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Publication Date
Mon Apr 17 2017
Journal Name
Wireless Personal Communications
ITPMAP: An Improved Three-Pass Mutual Authentication Protocol for Secure RFID Systems
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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of King Saud University - Science
Three iterative methods for solving second order nonlinear ODEs arising in physics
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Publication Date
Thu Jun 01 2023
Journal Name
Journal Of Engineering
A Control Program for Hydropower Operation Based on Minimizing the Principal Stress Values on the Dam Body: Mosul Dam Case Study
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This study examines the vibrations produced by hydropower operations to improve embankment dam safety. This study consists of two parts: In the first part, ANSYS-CFX was used to generate a three-dimensional (3-D) finite volume (FV) model to simulate a vertical Francis turbine unit in the Mosul hydropower plant. The pressure pattern result of the turbine model was transformed into the dam body to show how the turbine unit's operation affects the dam's stability. The upstream reservoir conditions, various flow rates, and fully open inlet gates were considered. In the second part of this study, a 3-D FE Mosul dam model was simulated using an ANSYS program. The operational turbine model's water pressure pattern is conveyed t

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Publication Date
Wed Dec 28 2022
Journal Name
Al–bahith Al–a'alami
Frames of Al-Alam TV channel’s handling of the Iraqi and Lebanese protests Analytical study of the main news bulletin for the period from October 1, 2019, to December 31, 2019
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        In October 2019, Iraq and Lebanon witnessed widespread protests, which aroused the interest of the media, as they began with demands for the provision of services, then escalated with the overthrow of the political system. The researchers chose a satellite channel that represents a direction for a country accused of entering the line of protests. This paper aims to analyze the main bulletin of Al-Alam channel to find out how it deals with the protests in the news. It is classified descriptively, using the survey method and the method of content analysis. The study community was represented by the main news bulletin of Al-Alam channel. The researchers adopted a deliberate sample for the period from 1/10/2019 to

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Publication Date
Mon May 09 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Choosing the Planning Aggregate Production strategy of the Organization of service - A Case Study in Baghdad hotel: Choosing the Planning Aggregate Production strategy of the Organization of service - A Case Study in Baghdad hotel
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Constitute a planning problem on the basis of personal experience and self-governance in the service organizations away from quantitative scientific method in planning an anchor and a platform, who made a recent research study, analysis and interpretation through scientific methodology adopted which formed its contents, The research aims to identify the true reality of production planning in service organizations, specifically in the Baghdad Hotel as a society to look, in order to assess the best strategy through the standard cost of the strategies of tracking and settlement to cope with developments on services demand changes, Search results confirmed that the settlement rates of production strategy is the best strategy in accordance wi

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Publication Date
Wed Mar 01 2006
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Environmental Auditing A proposed Framework For Practice In Industrial Companies: Practical Study In Iraqi State Company For Cement
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This research aims to studying and analyzing the theoretical
framework of the environmental auditing in industrial environment to its a broad and danger environmental effects . It aims to contribute in setting and testing a proposed procedure framework for environmental auditing in that vital activity .The practical aspect focused on testing a proposed framework within practice it in a one Iraqi industrial company that has a huge effect on environmental activity, represented by Iraqi state company

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Publication Date
Sun Apr 01 2018
Journal Name
Journal Of Educational And Psychological Researches
The obstacles that encounter a program of rehabilitating released prisoners as perceived by prisoners themselves in tubas' province
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The study intends to explore the obstacles that encounter a program of rehabilitating released prisoners as perceived by prisoners themselves in tubas' province. To this end, the researcher used a questionnaire as an instrument which was applied on (150) prisoner had chosen randomly to collect the study data. The findings revealed no significant differences among obstacles the encounter program regarding to the following variables: age, detention period, and number of detention, additionally, the findings found that there is a variance of obstacles mean according to the prisoners themselves, rehabilitation program, and the facility of that program.

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Publication Date
Thu May 14 2020
Journal Name
Journal Of Planner And Development
“The role of parametric approach in design highest climatic performance buildings: local housing design patterns as a sample”
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In light of increasing demand for energy consumption due to life complexity and its requirements, which reflected on architecture in type and size, Environmental challenges have emerged in the need to reduce emissions and power consumption within the construction sector. Which urged designers to improve the environmental performance of buildings by adopting new design approaches, Invest digital technology to facilitate design decision-making, in short time, effort and cost. Which doesn’t stop at the limits of acceptable efficiency, but extends to the level of (the highest performance), which doesn’t provide by traditional approaches that adopted by researchers and local institutions in their studies and architectural practices, limit

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