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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
Fri Apr 15 2022
Journal Name
Alustath Journal For Human And Social Sciences
The Intersectionality in I’ve Been Meaning To Tell You: A Letter to My Daughter: A Post-Colonial Perspective
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Intersectionality is a concept that focuses on social inequality towards black people and provides an analytical instruments for creating social justice issues in such a way in order to depict how social marginalization, or privilege occurs differently in various social positions. It does this by focusing on the interaction of multiple systems of oppression. Intersectionality is used to examines how the social factors; race, gender, and class can affect the people’s life especially the immigrants, black people, and refuges. This article will depicts how blacks in Canada are segregated and distinguished from white race. David Chariandy’s I’ve Been Meaning To Tell You: A Letter to My Daughter 2018 is analyzed through Kimberle Crenshaw

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Publication Date
Fri Jul 01 2022
Journal Name
Advanced Powder Technology
Modification of FAU zeolite as an active heterogeneous catalyst for biodiesel production and theoretical considerations for kinetic modeling
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Publication Date
Thu Feb 07 2019
Journal Name
Journal Of The College Of Education For Women
Nominal Ellipsis in English & Arabic and its Influence on the Translation of the Meanings of Some Selected Qurànic Verses ( A Contrastive study ): هدى فالح حسن & جمانة شكيب محمد
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Nominal ellipsis is a linguistic phenomenon found in English and Arabic .It is
based on leaving out a part of a nominal construction or more for the sake of good
style , compactness and connectedness .This phenomenon is found in the language of
the Glorious Qur’an .The study in hand is concerned with how translators handle
translating Qur’anic verses which contain ellipted nouns , i ,e. , to what extent the
translated Qur’anic verses are close to the original ones , and to what extent their
translations serve understanding the meanings of the glorious verses while at the
same time maintaining their beauty in style. The study aims at shedding light on
nominal ellipsis in English and Arabic .The study undertak

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Publication Date
Wed Nov 26 2025
Journal Name
Tikrit Journal Of Administrative And Economic sciences
Determination of competency levels and auditor evaluation procedures to the international standard (ISO19011: 2018) A case study at the Ministry of Construction, Housing and General Municipalities/Audit Directorate
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The current research seeks to achieve several objectives, including knowing the extent of the audit directorate of the Ministry of Construction, Housing and General Municipalities of the International Standard (ISO19011:2018) regarding determining the efficiency and evaluation of auditors and diagnosing the gap between requirements and application and knowing the reasons for not applying some of the items in the standard, starting from the problem, The field raised the following question (Does the audit directorate determine the efficiency and evaluation of auditors according to the standard ISO19011:2018?), and the importance of research lies in determining the return that can be achieved by the directorate through its application of stand

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Publication Date
Mon Sep 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Supervisory oversight role for the central bank to raise awareness of the banking supervisory: Applied Research in the Central Bank of Iraq and a sample of the Iraqi private banks
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Representing banking supervision An important function performed by the Iraqi Central Bank, in order to achieve stability in the financial and banking system, and safeguard the rights of depositors, investors and other targets, and to realize the Iraqi Central Bank banking supervision actors on banks, there must be an awareness of regulatory bank's existing control and subject them, as well as the role of banking oversight interested in spreading this awareness.
So sought search to find out the role played by the Iraqi Central Bank in raising awareness of the regulatory banking between the parties to the regulatory process, through the presentation and analysis of the legal framework for banking supervision and awareness supervisory

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Publication Date
Tue Oct 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
Determination of the lot size using the Wagner-Whitin algorithm under the Constraint Theory / Case Study of Diyala Public Company
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         International companies are striving to reduce their costs and increase their profits, and these trends have produced many methods and techniques to achieve these goals. these methods is heuristic and the other Optimization.. The research includes an attempt to adapt some of these techniques in the Iraqi companies, and these techniques are to determine the optimal lot size using the algorithms Wagner-Whitin under the theory of constraints. The research adopted the case study methodology to objectively identify the problem of research, namely determining lot size optimal for each of the products of electronic measurement laboratory in Diyala and in light of the bottlenecks in w

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Publication Date
Thu Mar 30 2023
Journal Name
Journal Of Economics And Administrative Sciences
The Role of Electronic Customer Trust Building Tools On Excellent Performance An analytical study of the opinions of a sample of individuals in the administrative and leadership positions in the Northern Cement Company
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The current study aims to overcome the conflicts facing the company in its way of staying and continuing to maintain its performance excellent in light of the intense competition, which made it seek to find strong ways and links with its customers through electronic communication using electronic platforms, and this put confidence and safety in The place of suspicion and fear of not fulfilling credibility or violating the privacy, so this research comes to answer about the question:  “Can the company achieve an excellent performance by relying on the customer's electronic confidence?”.

The study followed the descriptive and analytical approaches by providing a virtual model and testing the zero hypotheses, which stipulat

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Publication Date
Wed Oct 18 2023
Journal Name
Ieee Access
A New Imputation Technique Based a Multi-Spike Neural Network to Handle Missing Data in the Internet of Things Network (IoT)
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Publication Date
Sun Oct 01 2023
Journal Name
Asian Pacific Journal Of Cancer Prevention
Immunohistochemical study of the expressed cluster differentiation markers proteins type 20 and 56 in breast tissues from a group of Iraqi patients with breast cancers
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Publication Date
Sun Oct 19 2025
Journal Name
Lecture Notes In Networks And Systems
Analyzing the Pragmatics of Argumentation in the Arabic Novel Using Artificial Intelligence: An Applied Study on the Granada Trilogy
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