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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
Tue Jan 01 2019
Journal Name
African Journal Of Hospitality, Tourism And Leisure
Employing marketing information systems for the success of small and medium enterprises: A field study of some Tourism and Travel companies in Baghdad
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Publication Date
Sat Sep 24 2022
Journal Name
Arab World English Journal
A Critical Stylistic Study of the Notion of Women Empowerment in the Mona Lisa Smile (2003)
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This study unveils the ideologies of women empowerment encoded in the Mona Lisa Smile movie (2003). It reveals how the stereotypical image of women born only to be wives and do the duties of upbringing and housework is challenged. Katherine Ann Watson (Julia Roberts), the main character in the movie, wants to make a difference in the next generation of women. She rejects the imposed traditional ideologies. Linguistically, she opposes conventional thinking and seeks to persuade her students that life is about more than getting married. The primary focus of this study is to examine and clarify how the characters’ linguistic choices convey their ideologies concerning the notion of women empowerment. To do this, the researchers apply

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of The College Of Education For Women
The Problem of Paradox and its Manifestations: A Study in the Titles of Najm Wali's Novels
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The irony pushes us to inquire about what is in the text of contradiction, irony, suspense, and other acts of paradox, as well as a departure from what is logical, or familiar, that attracts the attention of the addressee, and this is what drives us to introspect the text and interrogate it in order to get to know the intended product of the text or its real or metaphorical intent. On the other hand, the irony is more in the literary text than in the scientific texts. Therefore, critics add the word literature to it in their definition.

 As it is represented by the paradox, we will seek to study the paradox of the title and the problematic that it may pose as the beginning of the text, and i

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Publication Date
Sat Dec 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Kinetic Modeling of Electromembrane Extraction of Copper using a Novel Electrolytic Cell Provided with a Supported Liquid Membrane
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   The aim of this study is to investigate the kinetics of copper removal from aqueous solutions using an electromembrane extraction (EME) system. To achieve this, a unique electrochemical cell design was adopted comprising two glass chambers, a supported liquid membrane (SLM), a graphite anode, and a stainless-steel cathode. The SLM consisted of a polypropylene flat membrane infused with 1-octanol as a solvent and bis(2-ethylhexyl) phosphate (DEHP) as a carrier. The impact of various factors on the kinetics constant rate was outlined, including the applied voltage, initial pH of the donor phase solution, and initial copper concentration. The results demonstrated a significant influence of the applied voltage on enhancing the rate of c

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Publication Date
Wed Mar 30 2022
Journal Name
College Of Islamic Sciences
Discretionary Punishment (Al-Ta'zir) for the Interest and its Effect in Keeping the Public Regulation A Fundamental Applied Study in the Saudi Arabian Courts
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Discretionary Punishment, Public Regulation, Interest

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Publication Date
Sat Jan 01 2022
Journal Name
Proceeding Of The 1st International Conference On Advanced Research In Pure And Applied Science (icarpas2021): Third Annual Conference Of Al-muthanna University/college Of Science
Efficient approach for solving high order (2+1)D-differential equation
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Publication Date
Thu Jun 15 2017
Journal Name
International Journal Of Computer Applications
Assessment of Annual Wind Energy Potential at Three Sites in Iraq for Wind Energy Applications
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Assessment of annual wind energy potential for three selected sites in Iraq has been analyzed in the present work. The wind velocities data from August 2014 to July 2015 were collected from the website of Weather Underground Organization (WUO) at stations elevation (35m, 32m, and 17m) for Baghdad, Najaf, and Kut Al-Hai respectively. Extrapolation of stations elevation and wind velocities was used to estimate wind velocities at (60m, 90m, and 120m). The objectives are to analyze the wind speed data and assess the wind energy potential for wind energy applications. Computer code for MATLAB software has been developed to solve the mathematical model. The results are presented as a monthly and annual average for wind velocities, standard deviat

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Publication Date
Thu Oct 01 2015
Journal Name
Journal Of Educational And Psychological Researches
Early marriage for the minors: a phenomenon of family violence against children
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It is certain that marriage has the favor of the continuity of human kind since the Prophet Adam till now. But this important event is threatened by some justifications which lead to its delay or abandonment. In the West, sexual relations, illegal friendships, and disrespect of marriage sacredness lead to this delay. While the reasons behind the delay of marriage in the Arab world refer to high dowries, women go out to work, and the religious and scientific ignorance of the need and importance of marriage. The problem also differs according to the difference between the rural and urban regions. On one hand, we find that early marriage is a necessity in the rural regions; on the other hand, the delay of marriage is a clear and nat

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Publication Date
Sun Dec 12 2010
Journal Name
Journal Of Planner And Development
The effect of pedestrian roads in providing a comfortable environment for humans
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Planning of cities show great attention on streets planning as one of the most structural component foundations for cities, that providing many functional needs and connect parts of the city each other, and work as a commercial and services activities centers. Instead of this highly focused on distributing streets with different streets types such as economical and trading and housing streets. This concerned was only on the dimensions and scales of different types of vehicles and their movement. When scale and dimension and movement of mans were as a second priority in designing and planning streets. Which came's first for traditional streets. The research try to submit some designs guides for planners that contribute in re conce

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Publication Date
Mon Jan 01 2024
Journal Name
Aip Conference Proceedings
The role of road elements in providing a safe environment for pedestrians
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In the years recently city planning projects have been confirmed sustainable high concentration on planning streets and pedestrian paths being the most prominent component of the urban structure in the city and these me and diverse departments link the city’s sectors and serve as a space for economic, service, and social activities. On the other hand, pedestrian traffic is an essential component of the various means of transportation within the city. Suffer cities in the Middle East and Arab cities in particular are neglecting pedestrian paths in the vital urban environment. Vehicle control mechanisms on roads, and changing the uses of pedestrian paths as result of encroaching on the sidewalks designated for pedestrians. Which leads to a

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